What kind of pump are you using.... one with a hose or one without a hose? In my experience those without a hose put stress on the stem while pumping which eventually results in the stem breaking loose from the tube. I ran into that very problem with presta tubes on last year's trip with a short frame pump... I have NEVER had it happen with my floor pump at home and I didn't have the problem with the Schrader values on the mountain bike I used on a 3,142 mile trip.
As such, a Lezyne Micro Floor Drive HP, a frame pump with a hose, was acquired for future trips.... It has a hose which will allow for daily "top offs" of tire pressure and for repairs without stressing the stem. Most of our bikes will continue to have more traditional frame pumps for on-the-road repair purposes. However, for daily top offs and repairs on the road the Lezyne will be the primary pump and at home the floor pump will be the primary pump.
BTW, this problem isn't something new... I recall back some 35+ years ago the LBS was very careful to show people how to use frame pumps with presta values to prevent breaking the stem. In those days Zefal and Silca frame pumps were common. Regarding technique, in addition to holding the tire and pump together while pumping the removal technique was to hit the pump away from the stem instead of twisting/pulling to remove it from the value. We never had problems... On the other hand, with the newer relatively low volume short pumps, which require about a 1,000 strokes to attain pressure, the problem is far worse.