Yes, definitely.
What follows is not an exhaustive list, but should give you some idea of the sort of discrepancies and mistakes that exist.
The most significant example comes from Goblet of Fire. In an early printing of the book, in the scene where Voldemort’s victims emerge from his wand, James came out before Lily, despite Lily having been killed more recently. This was revised in later printings.
See the question Why did Harry's father emerge before his mother in HP and the Goblet of Fire? for more details.
@DVK asked a question about six months ago about discrepancies between the main seven books, and the supplementary books Fantastic Beasts and Where to Find Them, Quidditch through the Ages and The Tales of Beedle the Bard.
My answer to Are there any discrepancies between HP1-HP7 and supplementary books? contains a list of the slip-ups that I know about.
Pottermore has also thrown up some discrepancies between the books, and the “word of God” additional text and interviews by JK Rowling. See @Slytherincess’s Meta question What is the best way to deal with complicated canon discrepancies when answering questions? which highlights one such example.
The Harry Potter Wiki isn’t generally considered canonical or accurate on this site, but their list of mistakes in the Harry Potter books is probably the closest to an exhaustive list that you’ll find. (Asking for the complete list on this site would almost certainly be closed as “too broad”.)
A running joke on this site is that JK Rowling’s maths is patchy, at best.
For example, dates just don’t work. We know from Nearly Headless Nick’s deathday party in Chamber of Secrets that the books take place in the 1990s, but then weekdays don’t match, and the time between dates isn’t consistent with any known calendar. (See my answer to Do wizards use the same calendar as muggles? for one such example.) Related to dates are ages, which are sometimes inconsistent from book-to-book. The HP Wiki has a more complete list of dating contradictions.
From an FAQ page on JK Rowling’s website, addressing one particular dating mistake:
Maths is not my strong suit (though it's better than my geography, as those who have found the most recent Easter Eggs might already know).
Another fairly obvious one is the size of the castle compared to the yearly intake. The school is far too small to merit such large premises, and the size of the magical population in Britain is unsustainably small.
Searching this site is bound to find you other examples of JK Rowling’s dodgy maths.
Finally, JK Rowling has acknowledged, on multiple occasions, that there are mistakes in the books. From another FAQ page on her website:
How do you remember everything from different books when you are still writing the HP series?
As obsessive fans will tell you, I do slip up! Several classrooms move floors mysteriously between books and these are the least serious continuity errors! Most of the fansites will point you in the direction of my mistakes. But the essentials remain consistent from book to book because the story has been plotted for a long time and it is clear in my mind.
