If you slipped, and there was like a small bite taken out of the pocket, you could fill that. But if you overshot it and the whole thing is loose, I'd rather see you make it flat, glue in a filler strip, and try again. Coating the whole side wall with filler is just kind of amateur. The fill can crack loose, too, since its in a high mobility area. There's more guitars with cracks around that area than anywhere else, even the trem stud area I'd wager. If you don't want to put wood in there, go ahead and fill it, but make darn sure it's a good filler, like an epoxy base. And don't try to mold the fill wet. Just get a lot on there and file/sand/route it after it's cured. Don't put the neck in there to squeeze the filler into the right shape either. It won't work. You'd have to put plastic wrap or wax paper on the neck to avoid adhesion. That would add its own dimension. Plus fill will usually shrink when curing.