Anyone ever found some of these in a video game, the series ends and your just left staring at the screen saying "...but...but...what about..."

I've only had it happen to me a couple times, but it has happened. The biggest one was the Jak series

Jak=Mar= Ancient Warrior that established the great Haven City in the distant past

Play these games and it just doesn't add up. Jak never put on the armor that Mar used to fight off the metal heads till after Haven City was built. IT'S JUST A HUGE WHOLE IN THEIR THAT DRIVES ME CRAZY!!!

Tater Salad
No, because Jak goes back in time again.

That series has more time travelling than Back to the Future. :/

Or Soul Reaver.

The only major plot hole I hated was in Jurrassic Park 2. How did the T-Rex kill everyone on board, and then get itself locked up again?

A combination of a tiny brain and a tiny pair of hands.
They're stupid, but they're also good with locks.

True Crime: Streets of LA had the biggest plot hole ever.

.: Myxomatosis :.

I find it ironic how a game with the smallest plot can have the biggest plot holes

..while the Metal Gear Solid series, which has a hell of a backstory, has little to no plot holes.

.: Myxomatosis :.

I think it's because plot heavy games generally both have more thought put into the story, and have more time story-wise in which to address potential plot holes.