There are a few things that might be going on here.
Sometimes the Piano Roll display decides to jump up vertically after you pencil in a note, so you may be pencilling in new notes in the wrong place. This would produce very obvious (probably higher) notes.
If the changes are the "tone" not note, it's probably a synth that changes its sound on purpose automatically over time, or that you have accidentally entered automation data (in the Piano Roll, or main Arrange tracks) that is changing parameters on the synth.
Read Chapter 10, Chapter 16 and Chapter 26 in the main Logic User Manual, and read the section for the particular plug-in synth you are using in the Logic Instruments and Effects manual. Then open the synth plug-in you are using and play around with its controls.