Yes, a CAI can cause a misfire.
If the intake diameter isn't quite what the MAF is calibrated for, you will get a different amount of air into the engine than it is metering.
If you get too much, then you can run lean and get misfires (pinging).
You also moved/disconnected/disabled at least one emissions related component for the intake (there are leftover hoses, right, and not just the butterfly?), well, if this is the case, they could contribute to misfires.
Finally, if you are just getting more air into the engine than the ECU is programmed to compensate for (the fuel maps are no longer correct), then a misfire can occur.
If I were a Toyota service person I would politely suggest putting in your stock airbox to see if the problem persisted. I'd even be nice enough to offer to install it for you (at the standard labor rate).
If the problem persisted after that I might be nice enough to cover it under warranty, but if I were having a bad day or if you rubbed me the wrong way some how, I would just say the problem was caused by the CAI that was there and warranty will not cover it.
So, if it were me, I'd put the stock airbox back in and see if the CEL disappears. If so, you hav ethe answer to your question. If not, go to Toyota and let them fix it, what they don't know can't hurt you.