There is a lot of reasons that can happen.
A few reasons I can think of:
1: The sample is not cut at a "0" crossing.
2: The sample is not at the proper BPM.
3: The sample is cut at a point where the audio does not flow from the end to beginning. For example, a crash hit towards the end of the sample, but you don't hear it at the beginning of the sample. So the crash does not appear to fade out naturally.