For clarity, when you say “the same flights,” do you mean the exact same sequence of flight numbers? Or do you mean, Google found the same physical flights, but using codeshared flights for at least one segment? (i.e., Google found, e.g., LH flight 123, and the United app found flight UA7923 operated by LH flight 123?) It makes a big difference to understanding why this is happening.

If you can give a sample itinerary (dates, cities, and times) when you’re seeing this behavior, someone can likely figure out what’s happening. There’s not enough to go on yet — airfare is extremely complicated.