This happens from time to time and is related to the Contamination deck not able to found by the script for various reasons. You can go to script delete lines 424 - 431 to stop this. After that you will manual have to shuffle the Contamination deck and the Intruder Bag.

These are the lines you want to delete

--Creates a Timer to shuffle the intruder bag if its contents change.
Timer.create({
identifier = 'shuffleCheckTimer',
function_name = 'shuffleCheck',
function_owner = self,
delay = 1,
repetitions = 0,
})

How to delete it ? I guess I need to go into "Modding" -> "Scripting" then search for the code to delete, but once I find it, if I press - (to comment) or select the lines and delete them, I just gte jumped further in the script.
I did press "Save and play" after and got the message : " Error in Script (Global): chunk_3:(978,0-1): unexpected symbol near '-' "

I just had this issue arise. It appears that if you flip the table then go back in time it clears the timer which stops the error.

I believe I found the solution. I've just posted it in the general bugs thread.

The zone for contamination cards overlaps with the discard. You can save the game with nothing in the discards, reload and it should ID the contamination pile correctly. or change the code as I did the following:

Line 2159:
if contaminationDeckGUID == nil then
contaminationDeckGUID = getDeckGUID(contaminationDeckZoneGUID)
end
if contaminationDeck ~= nil then

Line 2179:
if contaminationDeckGUID ~= nil then

ideally with this code change the zone area should be reduced a little so there isn't a conflict in the first place.

The the patch has completely changed this function and this error should no longer be a problem.