-Multiple sources of the truth. I've seen spreadsheets used in lieu of professional estimating tools for pricing jobs, and been abused because I wasn't use the "latest version" of the spreadsheet that got cc'ed around at 11pm called estimate July 24 v11a LATEST.xlsx
-Fudge factors and spaghetti formulas. You can take a nearly complete data set and essentially manipulate it to tell any story with inconsistent formulas, hidden columns, references from other sheets etc.
-VBA extends capabilities but is has some serious performance issues, doesn't implement objects correctly, doesn't handle errors well, code can't be version controlled.
-Gets used to do a poor job of purpose built software that the business has licenses for, like estimating/scheduling/MRP because of a lack of training.
-Business logic usually isn't apparent or documented and has to be reverse engineered to be understood.
-Propagates silos within businesses as they decentralise data and tend to diverge.