These physics/collision glitches seem to happen because of an apparent deficiency in the companion’s AI/pathfinding…
From time to time, your Runner just isn’t capable of walking to you normally, for whatever reason, so it will fast travel or warp to you…but, while doing so, their physics aren’t disabled, so if they warp under you, or through you, BAM, straight to the moon! To me it seems to be the worst when either the player is trying to wander around inside of a bunker complex, or ride a vehicle, while they have the dog deployed.
The companion’s pathfinding seems almost completely incompatible with interiors, like the other machines themselves to some extent, so rather than walking around inside wherever normally the companion is far more likely to warp between certain spots in the structure as the player moves about…and if they happen to collide, yeah, through the wall/floor/ceiling you go.
The terrain in the game, as in any open-world game, is pretty varied…so, it does make sense that the machines might have pathfinding issues. They all do, to some extent. So it is understandable for there to be issues, but it is a bit annoying at times. I’ve given up on letting the dog roam freely, pretty much ever. I’ll carry it, and only deploy it when it absolutely needs to be deployed, then pick it back up and carry on. Just a work-around to avoid the glitchiness, until improvements are made. Speaking of which, some supposedly were just recently, but I’ve not let him wander the bunkers to see just yet.
As for while riding a vehicle, the companion just can’t keep up. So, instead of even trying, it’ll usually get caught in a loop of warping to you. If you’re lucky, it’ll pop up to the left or right, or behind, but if it shows up ahead of you, or under you…probably going to hurt. I’m still on a lowly, plain old XB1, so I can’t reliably use any of the vehicles anyway, but I’ve witnessed enough Runner-related vehicle wrecks all the same…
It is pretty inconvenient to have to carry Dogmeat all the time, but it beats the alternatives I think—for now.
Of course, as you folks noticed, the companion and pretty much all other machines can also cause physics/collision glitches just by running (normally, not warping) into/through/over wrecks. I think quite a while back things got changed in regards to how machine wrecks go from being physical/loose to being static or semi-static, which (combined with the same for their knocked-off parts) seems to contribute greatly (terribly) to wrecks getting sent flying, too.