Are they Canon .mxf files?
I have that same issue with canon .mxf files from C70 and C300. Premiere doesn’t seem to know how to read that timecode properly causing it to get confused looking for clips. The only workaround I’ve found is to make new proxies through premiere, though that’s a pain when you already have proxies from the camera.
OR You may also notice playback in your timeline with those files is also stuttery and slow, in which case you should transcode them all to ProRes and edit with those files instead. That’s the only solution we’ve come up with until Adobe fixes it’s canon mxf support. (They know about the issue now, but haven’t said when it will be fixed).