Outright fakes are rare
Manufacturing a convincing mineral specimen is harder than finding one. Genuine fakes exist, mostly among high-value gem crystals and famous localities.
Bismuth hopper crystals sold as natural are the common exception, and they are laboratory-grown rather than mined.
Composites and repairs
Crystals glued back onto matrix, or onto a matrix they never grew on, are common and often undisclosed. Ultraviolet light frequently reveals adhesive that daylight hides.
Repair is acceptable when disclosed. The word to listen for is restored, and the follow-up question is how much.
Treatments to expect
Heating changes colour in amethyst and in many gem materials. Irradiation darkens quartz and blues topaz. Dyeing is common in agate. Oiling hides fractures.
None of this is fraudulent in itself, and all of it should appear on the label.
Three checks worth making
Look at the join between crystal and matrix under magnification: glue collects in a way natural growth does not, and often fluoresces under ultraviolet light. Check whether the crystals point in directions that make sense for a pocket rather than for a display.
Weigh anything suspiciously large for its species. Density is difficult to fake, and a specimen that feels wrong in the hand usually is. None of these is conclusive alone, and together they catch most of what circulates.