Common eye tracking problems
Glasses
Glasses are normally not a problem. Bifocal or varifocal glasses can be more problematic, but normal glasses are no obstacle for eye tracking. The only problem can be with reflections. If the orientation of the glasses is such that a clear reflection of the infra-red light source is visible eye tracking can be impossible. This can usually be solved by changing the angle of the glasses. Dirty or scratched glasses can be a problem too. Contact lenses are usually no problem at all.
The current MRI-compatible glasses use very small lenses, so it can be difficult to get to a point where the participant can see the entire screen, and the eye tracker can see the entire eye. Sometimes it is possible to get good data despite glasses, but it's probably wise to encourage your participants to wear contact lenses if they have any.
Makeup
Mascara can make eye tracking impossible, as the software will interpret the black regions in the picture as the pupil, and mascara is very black too. Mascara will always have to be removed, and it is best to ask people not to wear any mascara when they participate in an experiment involving eye tracking.
The same precautions apply to eyeliner, eyeshadow, etc. Makeup remover is available in MRI.
Drooping eyelids
Drooping eye lids can be a problem, as they can partly obscure the pupil. This is more common with older people. The solution is to move the camera to a lower position, if possible, so that the eye is filmed from below. If that doesn't help an eyelash curler can be used.
Asymmetries in tracking accuracy
There are typically left-right differences in (monocular) data. Eye tracking data will always be less reliable and distorted towards the edges of the screen, and the problems are more serious for the eye on the opposite side. Try to present your stimuli in the center section of the screen, if possible.