The BOLD signal is only an indirect measure of neural activity, and is therefore susceptible to influence by non-neural changes in the body.
BOLD signals are most strongly associated with the input to a given area rather than with the output. It is therefore possible (although unlikely) that a BOLD signal could be present in a given area even if there is no single unit activity.
fMRI has poor temporal resolution. The BOLD response peaks approximately 5 seconds after neuronal firing begins in an area. This means that it is hard to distinguish BOLD responses to different events which occur within a short time window. Careful experimental design can reduce this problem. Also, some research groups are attempting to combine fMRI signals that have relatively high spatial resolution with signals recorded with other techniques, electroencephalography (EEG) or magnetoencephalography (MEG), which have higher temporal resolution but worse spatial resolution.
fMRI has often been used to show activation localized to specific regions, thus minimizing the distributed nature of processing in neural networks. Several recent multivariate statistical techniques work around this issue by characterizing interactions between "active" regions found via traditional univariate techniques.
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