Why would an inspection company flag two NM 12 gauge wires going through the same joist hole?
What they're probably trying to flag...
The usual thing that gets cited for this is the second paragraph of NEC 334.80 (text from 2017, but this hasn't changed much -- 320.80 is a newer extension of it that applies to AC/BX):

Where more than two NM cables containing two or more
current-carrying conductors are installed, without maintaining
spacing between the cables, through the same opening in wood
framing that is to be sealed with thermal insulation, caulk, or
sealing foam, the allowable ampacity of each conductor shall
be adjusted in accordance with Table 310.15(B)(3)(a) and the
provisions of 310.15(A)(2), Exception, shall not apply.

...and why their cite's a swing and a miss
However, even though the 24&quot; exception (which is the exception cited in the quote above) is ruled out in this case, because ampacity adjustments on NM cables are permitted to be made from the 90°C column ampacity in the table by the first paragraph of that very same section:

The ampacity of Types NM, NMC, and NMS
cable shall be determined in accordance with 310.15. The
allowable ampacity shall not exceed that of a 60°C (140°F)
rated conductor. The 90°C (194°F) rating shall be permitted to
be used for ampacity adjustment and correction calculations,
provided the final calculated ampacity does not exceed that of
a 60°C (140°F) rated conductor. The ampacity of Types NM,
NMC, and NMS cable installed in cable trays shall be determined in accordance with 392.80(A).

As a result of that fact, we can start with the 25A 90°C ampacity of 14AWG copper (or the 30A figure for 12AWG copper), and then start adjusting it accordingly, based on the number of cables (really, current-carrying conductors) we have present:

3 /2 cables (6 CCCs): 80% adjustment, so 20A &gt; 15A (or 24A &gt; 20A)
4 /2 cables (8-9 CCCs): 70% adjustment, so 17.5A &gt; 15A (or 21A &gt; 20A)
More than that: 50% adjustment, so 12.5A &lt; 15A = now the adjustments limit ampacity

So, unless you're cramming 5 cables (whether /2 or /3, in most cases) into a single hole, or using archaic cables that lack 90°C rated insulation (all modern NM is NM-B, which means that the wire insulation is 90°C rated), then you're good to go.