For sure, the intonation is the first place to check. This is done by comparing the 12th, or better still the 19th fret harmonic against the fretted note. They should be very close on a tuner, with light to moderate touch. If the guitar is in need of attention, you may wish to have a guitar tech setup the instrument.
Also, it is totally possible for a strong player to pull sharp as much as 25 to 30 cents, simply by pressing too hard. This effect is exaggerated by action that is too high and is more prominent on the lower frets.
If the player is a Zakk fan, he may even be pinching out unintentional harmonics, which subscribe to a just tuning scheme and may seem out from the equal tempered notes used by the other instruments in the recording.
Bad strings or even bad frets can throw the tuning off. Action that is too low can cause the string to a catch a higher fret than intended, or even the pickup, which is bizarre sounding, but easy to identify at least...
Room nodes and higly notched/phased sounds can do strange things to the perceived pitch as well.
If the player does dig in too hard there, then a temporary solution is tune specifically for the context of this note to get the take.
Cheers,
Eric