More importantly, political slogans are not logical arguments, so one should not rely on them to prove things.
So the explanation for why this is not inconsistent is because “my body, my choice” has an unstated caveat.
Other's have already pointed out the false equivalence of this statement but for a moment let's ignore it.
Your logic here is that, again (incorrectly) assuming equivalence, that people that are pro-choice are being hypocrites by asserting a contradictory policy of a vaccine-mandate. The assumption here is that to avoid contradiction these people must either a.) reject their pro-choice beliefs or b.) reject their vaccine mandate belief...
but this is a gun with a barrel that points both ways... because the same hypocrisy holds for the person making this critique! If you are "pro-life" and anti-mandate you are also, according to this argument, in a position of contradiction. You can either a.) reject pro-life beliefs or b.) reject anti-mandate beliefs
By the internal logic of this argument either we have a vaccine mandate and have make abortion illegal, or don't have one and therefor never question a woman's right to choose again.
I have a sneaking suspicion that if everyone that holds the pro-choice/pro-mandate "contradiction" responded with to this issue with "you're right! forget the mandate, and I expect I'll never see another protest outside of an abortion clinic by anyone else against a mandate again!" many people relying on this argument would be quite upset.
This of course is really just demonstrating that the false equivalent is inherent because otherwise this contradiction would not be present in both sides of the argument. You can't evade hypocrisy simply by being the first to point it out.
You have to be more specific than mere "harm," which is the point of why I posted that. You need boundaries, clear ones, pre-defined and inviolable, else you are setting yourself up for the scenario which has already happened once in history.