When a stop is disabled (or has a train limit of 0), no trains are permitted to be dispatched to it. However, a train that is already at that stop is allowed to remain there.
When this mod makes a train scan train stops to check whether they are accessible, it does so by temporarily modifying its schedule. When it's done it removes the temporary stops it added and instructs the train to go to its previous destination. For a stopped train, this will be the station it is stopped at.
Because a train cannot be instructed to go to a stop that is disabled, if it was stopped at a disabled stop, it will enter a broken state where it waits for the stop that it is currently at to become enabled so that it can leave the stop and pathfind directly back to it. When the stop is enabled based on circuit behaviour this may not always be possible and risks deadlocking the network.
A fix should involve the scanning solution being changed to not touch a train's schedule at all. As a suggestion, a virtual train could be created at the same position as the current train, have the stops checked for accessibility, and then be destroyed. Alternatively, the base game's logic might already be exposed as an API that I missed.