It could be that the clip you're looping is not exactly starting & stopping on a measure.
Typically when making a loop I'll start the recording a little before and run a little after the beat 1 in the measure. Then I can go back, turn snap to grid on, then slip edit to the measure breaks before turning it into a loop.
The only thing that I have to be careful about is if I'm coming in a little before the measure (to drive the beat a bit). That said, I usually keep the original clip, copy and paste it to a new one to use to make the loop, and then mute the original one so I have it handy if needed.
Hope that helps.
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