When testing the PEMF with the vial tester from the mat's set, it only works on some spots of the crystals in the middle and not everywhere. Is it OK?

Several copper coils (2-10 depending on the size and model of the Bio-magnetic mat) generate pulsed magnetism PEMF. 

The crystals do not emit magnetism. They release infrared warmth and ions. But coils generate magnetic pulsations.

The intensity of magnetic fields falls with distance from the source as per the reverse square law.

Though the tester added into the set can detect PEMF only near the coil, it does not mean that there are no magnetic waves several inches away. It shows only that the tester is not sensitive enough to detect it there. 

Usually, we suggest these detectors to check if the PEMF coils function or not. 

To test correctly, make sure you do it immediately after you turn ON the PEMF feature. It works for 20-30 minutes with a sleeping period of 90-100 minutes before the next working cycle. It is essential to measure when the function is in the active phase.