Simple enough to reproduce, just let this map run for a while and the main loop will break.
Curiously, the error in the log doesn't seem to relate to PRPL directly, but without any cores on the map it doesn't have this problem.
NullReferenceException
at (wrapper managed-to-native) UnityEngine.Component:get_transform ()
at UnitManager.get_gameSpaceX () [0x00000] in <filename unknown>:0
at UnitManager.GameUpdate () [0x00000] in <filename unknown>:0
at Projectile.GameUpdate () [0x00000] in <filename unknown>:0
at CannonShot.GameUpdate () [0x00000] in <filename unknown>:0
at GameSpace.GameUpdate () [0x00000] in <filename unknown>:0
at GameSpace.Update () [0x00000] in <filename unknown>:0
system specs
Game version: 64 bit standalone Linux v 1.0.3b2
Computer: Arch Linux desktop, kernel version 4.7.8-1
CPU: AMD FX 4300
GPU: EVGA GeForce GTX 750
RAM: 8 GB
Looks like it was a problem with cannon shot destruction from multiple causes in the same frame. This would cause a "double" destruction which in turn would cause a "ghost" of a cannon shot in some internal data structures. Will be fixed in the next build.