The biggest one I've found, is after the trio escape from the wedding, and are attacked by two death eaters at the cafe in Tottenham Court Road :

Ron says "You're the boss. I've never done a memory charm before."
Hermione says "Nor have I. But I know the theory."

This is false, as she has already put a memory charm on her parents before. The other big one is the variation of the abilities of the Invisibility Cloak. While it is clearly mentioned that spells don't work on it, it doesn't mention how Moody could see through it.

EDIT : A lot of users have commented that the above is not a plothole because - the charm that Hermione uses on her parents is a memory modification charm, while the charm that Hermione prepares to use on Dolohov is a memory deletion charm. A couple of users have also mentioned that the two charms have different incantations and are not the same.

So, I spent a lot of hours poring over Chamber of Secrets and Deathly Hallows to find more information about the two different types of memory charms and to check if they really did have two different incantations. But I never did find any, so I left it that. So imagine my surprise when I was reading Goblet of Fire just now, and I found this gem which should put all the arguments at rest :

This just after Harry, Hermione and the Weasleys reach the site of the Quidditch World Cup and talk to Mr. Roberts, the muggle incharge of their tents. Mr. Roberts is getting very suspicious of all the wizards apparating around him and he engages in conversation with Arthur Weasley.

Harry Potter and the Goblet Of Fire, Chapter 7 : Bagman and Crouch.

“Ah—right—certainly—” said Mr. Weasley. He retreated a short distance from the cottage and beckoned Harry toward him. “Help me, Harry,” he muttered, pulling a roll of Muggle money from his pocket and starting to peel the notes apart. “This one's a—a—a ten? Ah yes, I see the little number on it now... So this is a five?”
“A twenty,” Harry corrected him in an undertone, uncomfortably aware of Mr. Roberts trying to catch every word.
“Ah yes, so it is... I don't know, these little bits of paper...”
“You foreign?” said Mr. Roberts as Mr. Weasley returned with the correct notes.
“Foreign?” repeated Mr. Weasley, puzzled.
“You're not the first one who's had trouble with money,” said Mr. Roberts, scrutinizing Mr. Weasley closely. “I had two try and pay me with great gold coins the size of hubcaps ten minutes ago.”
“Did you really?” said Mr. Weasley nervously.
Mr. Roberts rummaged around in a tin for some change.
“Never been this crowded,” he said suddenly, looking out over the misty field again. “Hundreds of pre-bookings. People usually just turn up...”
“Is that right?” said Mr. Weasley, his hand held out for his change, but Mr. Roberts didn't give it to him.
“Aye,” he said thoughtfully. “People from all over. Loads of foreigners. And not just foreigners. Weirdos, you know? There's a bloke walking 'round in a kilt and a poncho.”
“Shouldn't he?” said Mr. Weasley anxiously
“It's like some sort of... I dunno ...like some sort of rally,” said Mr. Roberts. “They all seem to know each other. Like a big party.”
At that moment, a wizard in plus-fours appeared out of thin air next to Mr. Roberts's front door.
“Obliviate!” he said sharply, pointing his wand at Mr. Roberts.
Instantly, Mr. Roberts's eyes slid out of focus, his brows unknitted, and a took of dreamy unconcern fell over his face. Harry recognized the symptoms of one who had just had his memory modified.
“A map of the campsite for you,” Mr. Roberts said placidly to Mr. Weasley. “And your change.”
“Thanks very much,” said Mr. Weasley.

Right there, the guy from the Ministry performs a memory modification charm on Mr. Roberts, and yet he uses the Obliviate charm. So now, we can be sure that both the Memory modification charm and the Memory loss charms are the same thing. So like I said, the Hermione in Tottenham Court Road scene is in fact, a plot hole.

Further discussions welcome.

I'd also like to clarify some of the 'plot holes' mentioned here.

1. Why didn't the twins notice Peter sleeping with Ron everyday?

A. The map is surrounded by moving dots of people. The only thing Fred and George are interested in are secret passages. Once they found all of them, they didn't really care. If you got a live map of your school, would you really be focusing on who is sitting next to your sibling?

2. Why couldn't Harry see the thestrals?

A. The death had to sink in. Harry was only a baby when his parents died, and most probably, he didn't even see them die, only heard them. After he saw Cedric die, he returned to Privet Drive where he was racked with nightmares about Cedric. So we can assume that the death sunk in at that point.

3. Why couldn't *random character* use the Time Turner?

A. You know what the most dangerous form of magic is? The unforgivable curses? Nope, it's Space and Time. And you do not mess with space and time. Read the part where the death eater gets caught up in a time jar during the battle ministry battle in OOTP and find out.

4. Why couldn't Sirius Black use the polyjuice potion?

A. He's an animagus. The potion only works for full-humans. Same reason why Hagrid and Lupin couldn't take it. Same reason why Rita didn't take it when she came to spy on the champions.

EDIT : A lot of people have pointed out that Sirius being an animagus does not make him a part-human. So I will concede that this is in fact a plot hole, unless JKR makes a statement that says otherwise.

5. Why did'nt anyone know of Hermione's "cat condition" from CoS?

A. Frankly, nobody gives a damn about the hospital wing. You're hurt, you go to Madam Pomfrey. She's seen a hundred different things, and she just doesn't care. Like they said "Madam Pomfrey doesn't ask too many questions." Which is the best thing a matron could do.

6. Why didn't they use Veritaserum to prove Sirius's innocence?

A. It takes too long to brew. And they had a bucketload of evidence to convict him, and he believed to have killed Pettigrew himself, so he went in without making a hue and cry. So when Sirius went in to Azkaban, he believed he was guilty of killing Peter. When you've got a murderer surrendering, you don't make him swallow a truth potion to admit stuff because that's what he's doing already.

7. Why was Oliver Wood captain for more than one year?

A. Dude, what?

8. Cho Chang had already finished schooling, yet she was back for the Battle of Hogwarts.

A. So were Fred and George, Oliver Wood, the entire Order of the Phoenix, the death eaters and Voldemort.

9. If Grinderlwald is the true master of the Elder Wand, why was he defeated by Dumbledore?

A. Grindelwald stunned the previous master Gregorovitch, and was owner of the Elder Wand. But, the fact remains that Dumbledore was stronger than Grindelwald. The Elder Wand knows weakness when it sees it. It isn't loyal to its master. The minute Grindelwald and Dumbledore started duelling, the Elder Wand knew that its owner was the weaker of the two, and it bent to Dumbledore's will, thus allowing him to beat Grindelwald. It's a bit difficult to get your head over, but that's how it is. If you want to be the true owner of the Elder Wand, you need to earn it by remaining strong in the face of your adversary, something which Grindelwald failed at.

10. How could Harry get immobilised under the Invisibility Cloak if it was supposed to protect him from harm?

A. So I finished reading The Deathly Hallows again yesterday, and I understand what the Cloak actually does. See, the power of a true invisibility cloak is to give the wearer complete and inpenetrable concealment. This is supposed to mean that whatever spells you threw at the cloak, it would still protect the wearer. Even if you tried to Accio the cloak to you or set it on fire, it wouldn't lose its powers of invisibility. It never states it would protect the wearer from spells designed to attack, which is evident when Draco attacks Harry in the Hogwarts Express in HBP or Dumbledore immobilising him, again in HBP. The cloak only conceals the wearer, it doesn't protect them from harm.