1. The record is incomplete due to burial, erosion, etc.
2. Much, if not all, are metamorphosed
3. There are (for the most part) no fossils to help with depositional environments or age dating
4. Things worked differently in the Precambrian: limestones were formed different, dolomites may have been primary, detrital systems did not behave the same way (lack of meandering fluvial, for example), reduced atmosphere that enabled mobile Iron that made banded-iron formations, some igneous rocks only formed then and do not form today (i.e. kimberlites), etc