One possibility is a blunder where two identical samples generate different results. Lab A didn't follow protocol, or a reagent was a bit old, or a power glitch or similar. This is independent of whether they are using the same method, same loci, etc.

This type of error is common enough that there are special checks routinely included. This might be a "standard" sample run in the same batch. They know what result the standard is supposed to have so if it's wrong then your sample may also be wrong.

Of course that doesn't fix a different kind of blunder where your sample got mislabelled or switched, or spoiled while in shipping. Those get checked by blind "traveller" standards. That's where occasionally the lab QA person mails a standard in labelled just like a normal sample. It's not a perfect check because it just detects sloppy handling of the traveller, not sloppy handling of your sample. But it does serve to weed out systematic problems

Another possibility is a random match or mismatch. If a given loci is expected to be present in, say, 50% of the population, and there's no correlation between loci, then the chance that two different sources match at 23 loci (but not the 24th). is around 1/2^24,. Which is one in about 16 million.