Entering SOI of certain planetary bodies can sometimes glitch out engines

This usually occurs with either Mars/Cylero-like bodies, but predominantly PS bodies made using the "Martian" template. When entering the SOI at very high speeds (usually above 50k meters/sec, although this is random) can just straight up break engines, especially engine clusters like my Comet Head's 3rd stage (pictured).
The engines will shut off (although remain active) when entering the SOI, and strangely the atmospheric vapor effects will appear for a brief amount of time. Afterwards, only the "top half" (when viewed directly from the rear of the craft) will function, and the craft will be stuck forever in a circular orbit around the planet. Using time warp will set the velocity to 0 m/s, too.
I'm unsure if this is a bug with these types of planets or the craft itself. The bug happened with 2 of my upcoming planetary bodies in my Mortan System too, which also used the martian template (would publish the bug report with a pre-public 1.2 Mortan but it might be unstable, wonky and/or may not work properly), and it also occured with another OP craft of mine while doing basically the same thing.
For instructions to recreate, the craft is lined up to enter ESS 4.0 Cylero SOI in a short amount of time, and may or may not bug depending on luck, device, and more. While this body hasn't shown any effects of the bug, it is the closest one i could get to something like the martian template, without using a buggy pre-pubic 1.2 Mortan, as mentioned before.