Yeah it's quite likely that your turbo might actually be causing the ECU to hit R&R (rich and retarded). This is where the airflow the AFM is reading exceeds what the ECU has been told is 'safe' and therefore shits itself and goes into damage control by dumping extra fuel in and retarding ignition timing.
Stock boost for an R33 GTS-T is 5psi up until 4500rpm, at which point it increases to 7psi. If you're running a boost controller of any kind, it should be used IN PLACE of the stock solenoid. Roughly 10psi is a safe limit to aim for, as the it will prolong the life of the turbo (as opposed to anything above 10psi lol) and should in 99% of cases avoid triggering R&R.
If you're sure the boost isn't exceeding around 10psi, then perhaps the cause of the misfire could be either spark plugs or coilpacks. If you have a stock turbo, it's more likely to be the plugs being old and wanting replacement. Other than this being fiddly as all f**k, the spark plugs are like $5 each lol. You're after NGK plugs, part number BCPR6ES (or just get the Bosche equiv, can't remember their part number off hand). These plugs are just heat range 6 and 0.8mm gap.
Should the plugs not fix the problem, then it's likely your coilpacks as suggested - assuming they too are stock items. After this many years of heat cycling, the silicone breaks down and allows the spark to escape through the cracked plastic body of the coilpack and earth out on the head, rather than flowing through to the spark plug and doing its job lol