I have been downloading midi files of tracks to create backing tracks and I mainly use virtual instruments that work inside Kontakt, with the exception of ez drummer 2. I have been having an issue where some of the Kontakt instruments when played back are transposed close to a half step or a half step higher. I cannot figure out what the issue is and how to prevent it in the feature. I do mainly now use Logic Pro X but I think I had the same issue in Pro Tools.

Sounds like a sample rate issue. 44.1kHz samples played at 48kHz will be pitched higher unless compensated somehow. There are workarounds in every DAW.

I think it may be my keyboard or something with Logic itself because also effect the stock plugins as well?

Check the basics first.