Perhaps the glass sheet is cracking due to thermal stress.
The laser deposits (a tremendous amount of) energy into the engraved area, the temperature goes up, the middle of the sheet expands more than the perimeter, and it cracks.
@jkwilborn found that out the hard way while engraving a slate sheet:
If you can’t change to a stronger glass, then you must reduce the amount of energy dumped into the sheet. Dividing the overall pattern into smaller sections and allowing the sheet to cool between each section may reduce the stress enough to get through the job.
How large-area engraving will affect the glass sheet’s properties in use is a good question. If the engraving leaves residual stresses, the whole sheet may shatter when somebody slams the cabinet door.
Maybe this is a job better done with acrylic panels, rather than glass.