It is quite possible to bend the yoke, especially if the OP used a vice, and in doing so, applied pressure while the two sides of the yoke were not exactly perpendicular to the vise jaws or the drift used was not parallel to the two caps. It has been done before this way, and a GOOD way to bend the yoke.

I never use a vise for this reason. I always hold the yoke in-hand (not clamped) and hit the caps in both directions with a SMALL balpene hammer to free them up, then hammer sharply but not hard with quick repetitive taps, out one way then turn around and tap out the other way.

Picture the cap moving in the bore while the yoke is pivoting about the shaft mounting flange. It flexes inward with any amount of force, and a hammer tap will apply force then relieve the force as the cap moves in the bore. Constant force applied will continue to bend the yoke, even when the cap is moving out of the bore, unless you back off on the force before you go beyond the metals elastic point, it will bend.

The yoke steel is a soft material compared to the U-Joint caps, and if there's any slight amount of skew of the cap in the bore the cap will dig into the softer steel and gouge the bore, since more pressure will cause a non-parellel force applied as the yoke bends. With sufficient force applied IF this happens, you will get the cap out and bend the yoke at the same time.