What makes it sketchy
A fair backcharge clause solves a real jobsite problem: if a subcontractor refuses to fix defective or incomplete work, the GC needs a way to keep the job moving.
A sketchy version skips the process. The shop finds out after payment is reduced, with no chance to inspect, fix, or dispute the charge.
The process you want
The GC should identify the issue, give written notice, allow a reasonable chance to cure, and provide backup for the cost.
If the problem is an emergency, the contract can handle that separately. But ordinary cleanup and coordination should not become surprise deductions.