Perhaps because Qualcomm (voluntarily) legally bound itself to provide licenses under FRAND terms as a condition for including their patents in the standard? Apple did no such thing.
I'm not saying Apple is in the right here. It actually sounds like they're screwing their suppliers, since their suppliers are the ones who have the licenses from Qualcomm, and it's those suppliers who are withholding royalty payments to Qualcomm on account of Apple not paying the money owed to them to cover their licensing fees. That said, Qualcomm is currently being investigated and/or sued by regulatory agencies around the globe for failing to abide by the FRAND terms they agreed to, so it seems safe to suggest that everyone's in the wrong at this point: Qualcomm for not abiding by its legal obligations, and Apple for not abiding by its contractual obligations.
Except in this case I think the reason is Apple is putting pressure on Qualcomm to settle.
Remember, Qualcomm is suing Apple because they believe Apple has crippled their chips to make them look bad. (Partly true - Apple has speed- limited the Qualcomm based iPhones so they perform similar to the Intel based iPhones). Qualcomm wants Apple to end this because they want people to seek out and buy the Qualcomm iPhones and thus get more royalties.
Apple countersued, saying that Qualcomm's royalty rates are out of line with industry standard, especially on the FRAND patents (and there are plenty of patents that Qualcomm will not license at all, much of which is related to why Qualcomm chipsets perform so much better than the competition).
It's a nasty set of arguments, and Apple's pressuring Qualcomm to come to a settlement by withholding payments until a decision is reached. The money is being paid, but to a trust account so Apple's not saving a single dime, it's just that the money is not being given to Qualcomm.
Eventually the case will have to be heard by the courts or Qualcomm and Apple kiss and make up and come to an agreement. In the meantime, Apple's not funding Qualcomm's lawyers against themselves.