At least in Italy, movement was restricted inside regions (sometimes provinces) of the same country due to the epidemy.
It's not nice for anyone involved, but the primary goal is to stop/limit the contagion. I'm an expat, so it goes against one of my interests, but I'm in favor of limiting border crossings, unless you can show that you won't spread COVID around.
So I think in this case (we are in a global pandemic) it makes sense to see freedom of movement not in a binary way (yes/no) but more in shades: allow more movement of more people as we get better at containing the pandemic.
Also please note EU is not a federal state, nor many of the founding members want that to be. So countries have a lot of power to decide how to handle pandemic. Still I think EU as a block did a good job negotiating vaccines in the context of not having a unity or a fast decision process.
So while I don't agree with restricting rights, I also don't agree with restricting rights of people who can move (like the ones vaccinated or immunised naturally) just because everybody cannot do it (cannot get vaccinated for personal or medical reasons).
And "random" it might be as much as 50% of the passing cars.