You describe a "crackling" sound. my guess would be that the linoleum floor has either come loose or is only partially stuck down in spots. You step down and the linoleum "sticks" a little and then crackles as it pulls up. It is ok to nail subfloor to joists so long as you use the proper ring nails and glue and stick to the proper nailing schedule (put in enough nails). by putting wedges in your builder has very likely loosened the connection between the subfloor and the joist(s). Unfortunately, he may have also "popped" 1 or more nails. I would insist that he pull out all the shims(after forcing subfloor glue into the new gaps), pull the linoleum, check for "popped" nails and re-fasten the affected area. Then he can put down the lino floor in a correct manner, which would have avoided this whole mess in the first place. I can't be 100% certain because I can't see it, but this is my best guess.