As others have said, the TP Lines app is consistently more accurate that the
MDE app, as Disney is overestimating wait times to cut down on long queues that overflow into the park. Given normal operations, the WDW app seemed to overstate actual wait times by 15-30 minutes, while the Lines app was pretty spot-on.
For example: when Pirates had a posted wait of 45 minutes, TP estimated 19 and we were on in 17.
When Alien Swirling Saucers had a posted wait of 45 minutes, TP estimated 25 and we were on in 27.
Disney is overstating wait times because the standby queues were not physically designed to hold the entire capacity. Kilimnjaro Safaris standby queue may only hold 1,500 people, so when there are 3,000 people in line (a 1-hour wait) it wraps all around Africa -- even into ugly backstage areas! It's causing major crowd control headaches now that they are ramping up capacity and grabbing dollars before they can actually support those crowd levels.
All that said, there are exceptions, mostly related to ride closures. If a major people-eater goes down, wait times at nearby attractions do increase, and the Lines app won't necessarily adjust for that in real-time. We headed toward Gran Fiesta Tour when TP Lines predicted a 10-minute wait, but noticed that Frozen Ever After was down. Sure enough, the queue for Gran Fiesta Tour really was 45+ minutes, as every hot, tired, cranky parent in the FEA queue took their hot, tired, cranky kiddos to the nearest ride. (We didn't even both to get in that queue.)