Why do some apps on my computer think time is going faster than it should be?

The developer of Marble Marcher is aware of the problem but they wrote: "There is currently no further major development planned for this game. Please submit issues and pull requests to the Marble Marcher Community Edition repository instead."

You can report the BOINC bug here but according to wiki the latest version is 5 years old so I doubt that they are actively working on it.

The reason is probably that this software wasn't written to take modern fast CPU's with many threads and cores into account.

In old games, and certain bad games like Fallout76, physics are tied to the framerate. For an explanation why read this and that.