We see on 44b that according to חכמים we kill the animal that is hefker and Rabbi Yehuda disagrees.
When we learned 13b, we saw Rabbi Yehuda's opinion there but it was quoted by Ravina, so one could have thought that this was according to everyone (even though Rabbi Yehuda is brought there as proof for this).
The Rambam paskens both sugyos. In 8:4 he paskens that a shor hefker is patur when it does damages using pasuk of שור רעהו. But the Rambam paskens like חכמים in our sugya and (10:6) and says that we kill a shor hefker
The Lechem Mishne and others point out that there is no contradiction. The sugya on 13b is discussing damage while our sugya discussed death. Even though Rabbi Yehuda is brought as proof by Ravina, the petur of shor hefker by nezikin is according to everyone.
Perhaps we can suggest that according to חכמים , when we kill the shor we are not killing it as a punishment for the owner but to remove a dangerous being from the world but in the case of nezek, if there are no owners we have no one to punish. Rabbi Yehuda could be saying that even in killing, the focus is on the owner who did not guard.
However, this explanation does not cover the case of a shor that damages and then the owner is mafkir, where even here the former owners are not liable.