I think originally we believed that this API does not fail for transient reasons. - Like if we set arguments correctly, have permissions to use it, etc... then it would always work.

We generally can't "handle" a failure in an API that we use to suspend threads. We can hope that some other mechanism, like hijacking, will work.
We can also hope that the reason for API failure is transient and will not repeat (for this GC or for the next one), but if it is because of shortage of memory, the shortage may not resolve until the GC we are trying to do happens.

I guess we can ignore the failure. Not a lot of options. There is a chance the test will switch from occasional failure to occasional timeout.
One way to find out. Perhaps it is indeed because of stressful environment while running many tests at once and the condition does not happen often or does not last long.