It either did not cure out before application of tile or there were holes in the glue where non was applied.
This should be very conspicous during the winter, but stop in the summer.
I would bring out the contractor and see if any recourse, which I will say with confidence, they will not help you. And, I do not think there is a remedy for this.
Mastic is applied by a trowel with knotched teeth. Mastic needs to cure or air out before applying tile. Sometimes 20 minutes or so.
There also could have been powder or debris on the floor that acted like flour on a rolling pin that kept the mastic from sticking to the subfloor.
If the tile is self stick, then the tile's glue was defective or debris got on it too.
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