discrepancy

  1. There is a discrepancy between inventory figures and actual stock.
  2. There are some discrepancies between inventory figures and actual stock.
    Which one is correct?

They are both correct and I think have the same meaning.

I would understand those as follows:
a discrepancy - one overall discrepancy in the final numbers.
some discrepancies - a number of discrepancies within the set of figures.