I will start by stating that this happened in a completely vanilla setting (no mods, no steamodded) and that it happened by accident and I am uncertain on exactly how to replicate it. There is also a lot of variables that affect exactly how the glitch behaves, I am typing this out and testing further at the same time.
However, it seems to only happen from launching the game, perhaps not being possible if done after opening the pause menu (I have pulled off the glitch more consistently from a fresh launch than from starting a new run via the normal method). Holding 'r' to restart a run does not stop the glitch from occuring.
The effect persists through reopening the deck view and reloading the saved run if and only if you did not draw any cards affected by the debuff (The first time it happened, I also coincidentally drew 0 clubs). This can be done much more consistently against the pillar.
All I can really say about the cause is that I clicked on the "View Deck" upon entering the Boss Blind (Club in this case).
Clicking on the debuffed cards in the deck view immediately applied the X, correcting the issue.