They definitely aired them out of order because you see them move to the docks after the warehouse gets found, then later you see them back in the warehouse.
The production order is also not the correct order to watch them in, although it's nice as a reference. Very few shows actually make the episodes in order. I base this partly on the 'previously's' for each episode (but I'm thinking of ignoring them as they don't appear to match up either) and Winter's base location.
The base location and Bo/Tate's relationship seems like the best thing to go off but I need to go through each episode with a fine tooth comb and that will take time and I've only been on it a very short while.
The only things I've definitely confirmed are the Pilot is first (duh) and the last four episodes are Prodigy, Collapse, Revelation and Second Chance, which also matches the production order.
To be honest I can live with the base location discrepancies. I'm mainly trying to work out where this additional episode 13, non-finale fits in. It appears to be after Defection and in the earlier part of the season, but I need to look into it more.
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