Could paint build up on a bottom bracket be considered a warranty issue?
It is normal and acceptable for a frame to be delivered with paint needing to be removed from the bottom bracket shell, headtube, and seat tube areas.

It is assumed that a qualified mechanic with appropriate tools available will be assembling the bike, and that preparation of the frame is simply one of the necessary steps in the build process.

Indeed, most every bike company requires that the frame be assembled by a qualified mechanic (and in some cases by a mechanic certified by the bike brand) in order to maintain the warranty on the frame or the bike.

Unless there is something preventing the frame from being prepared properly, then this is unlikely to be considered a warranty issue.