Are there currently any archaeological sites that we have little to no idea of what their significance/purpose is?

I could argue that we do not fully understand the symbolic meaning and use behind the temple groups, known colloquially as guachimontones, of the highland lakes region of Jalisco, Mexico and surrounding regions. There are some ceramic models from the nearby Nayarit region which depict a simplified guachimonton with a pole in the center. This had lead some researchers to believe that the temple groups were used for some sort of pole ceremony. Unfortunately due to the lack of extensive excavations of other sites and rampant looting in the region, it may be difficult to impossible to tell if the central structures or spaces actually contained post holes for such a ceremony. Even household groups consisting of four platforms arranged around a central space have not been excavated. For all we know the post holes are in those spaces rather than in the central altar of the larger structures. The leading hypothesis is that the temple groups were places of shared power in a corporate society. Each platform may have been associated with a different family/clan/lineage who participated in the construction of the guachimonton (my thesis is aimed to prove this hypothesis through architectural energetics and labor organizational models). There does seem to be concentrations of one type of artifact per platform like particular ceramics or an abundance of lithic debitage. What this means is still unclear because we need a larger sample size with more excavations.