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Yeah, it's not being hacked, it's a site bug that's been around for a few years and is very difficult to track. In the short term, don't keep a tab open to your anime list and never hit the back button to go back to your list or to an anime page where you just marked an entry.
For the first time in a few years we finally think we know how to fix it - you can follow the progress here: http://www.anime-planet.com/forum/feature-requests-bug-reporting-site-questions/193647-bug-episode-count-messed-up.html
Is it because your anime list changes on its own that you think it's been hacked?