The title of this post is a bit misleading; it shouldn’t be “if” problems arise but rather “when” they do. I can almost guarantee that you will uncover certain issues during due diligence that were not previously tabled. These can be outright misrepresentations by the seller (i.e. customer contracts that are in jeopardy), or other items you uncover in your research that give you cause for concern about the future viability of the business.
The one thing you do not want to do is run to the seller or broker every time there’s a problem expecting a deal concession. Doing so will cause the seller to not recognize the severity of any single issue and will likely give the impression that the buyer is looking for every excuse to either reduce the price or not do the deal at all.