Breathalysers only estimate the BAC, not physically measure it, so several factors can cause the breathalyser to give either an artificially higher or lower reading.

The most common are:
Body temperature and blood composition as outlined above.
Breathalysers assume that the alcohol concentration in the breath will be the same as in the blood, and that the breath is sourced from deep in the lungs, but the breath alcohol concentration can be increased by vomit or blood in the mouth, acid reflux, or simply having had a drink recently with alcohol residue from that drink still being in the mouth at the time of testing. Mouthwash or breath freshener often contain alcohol, so don't use these in an attempt to disguise the smell of alcohol when being pulled over.
Absorption of alcohol into the blood may lag actually drinking it by as much as 1-2 hours so even though you may have alcohol in your breath, if you've only consumed it recently it may not be in your bloodstream in the concentration that testing your breath indicates.
Item of Interest

Safe Drive Breathalyzer
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