Used silicone instead of grout

This doesn't sound like a good job has been done. You can tile onto plywood it use to be standard practise but nowadays any decent tiler will overboard the floor first with cement backerboard not plywood. You can still use plywood but must use the correct adhesive. It could also be that the tiles have not been put down wrong so there is not a decent level of adhesive coverage in contact with the tile. If you pop up any of the tiles and there are thin ridges of adhesive on the tiles with gaps between and not one solid layer of adhesive then they have not been installed correctly. This is the adhesive btw not the grout, grout is not what is used to hold the tiles down.

sack the builder for starters using silicone as grout is just his way of trying to stop a poorly laid floor from cracking for a while if joints are cracking out there is movement or flex in the floor and the builder knows this thats why hes tried to hide it with silicone eventually the flexing of the boards will loosen the tiles wooden floors should be prepared properly floorboards normally 18mmm thick should be over boarded with either minimum 18mm plywood or 6mm tile backer boards and if flooring grade chipboard is your subfloor again 18mm ply or tilebacker boards should of been used if overboarded with ply then two part flexible adhesive used and single part flexible for tilebacker board and flexible grout using silicone just temporarily masks the problem