I think this has started happening since the last mod update.

When bots are deconstructing cargo wagons and their contents, time usage by the mod goes very high for a split second every time a bot picks something up.
If the wagon is full, then this can cause a constant slowdown until the wagon is empty.

Are you marking the cargo wagon for deconstruction or waiting for the train to empty all the un-filtered slots ?

I should have clarified:
I'm not using the Equipment Grid Logistic Module on the trains at all. (Just on spidertron and aircraft)
The cargo wagon and locomotive should therefore act like vanilla as bots will not collect from the un-filtered slots.

The cargo wagon is filtered.
I am using a standard deconstruction planner.
The high time usage happens everytime items are picked up from the wagon, and when the wagon itself is deconstructed.
The high time usage also happens when manually picking up the wagon.
There is no slowdown when deconstructing/picking up the locomotive.

I use the events 'on_pre_player_mined_item' / 'on_robot_pre_mined' to capture when something is trying to decom one of the entities I am monitoring. Its been in the code for 7+ months. With these events I get given the entity being mined so I can make sure to disable the logistics module, or you could end up in a loop with robots bringing new items, while others are trying to take them away. However when you decom a train every time a robot takes an item from it, the event gets called.

I will see what I can do, maybe there is a way to exit out of the function early. Or I can investigate a recently added feature register_on_entity_destroyed and capture that event instead.