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As already suggested above, double check that 'Trinket Interactions' are enable in the settings.

I am having the exact same issue and trinkets I have place before have become unable to be changed. I bought my ships some time ago and this is happening on all of them. It might be a coding error or something.

@d3adst1ck I'm not getting the prompt at all and it is my ship because the Pirate lord ghost is telling me to put the trinkets down

When you say you can't place them, are you not getting the prompt at all or that they aren't being placed after selecting them?

If you aren't getting the prompt, check that 1) You're on a captain ship, 2) You have trinket interactions turned ON in the Gameplay settings.

Me and my lady are experiencing the same thing, I bought the sloop and is my vessel with a name and everything. But I cannot places in the trinket on the entirety of the ship, I even bought all sizes of trinkets hoping that would fix it.
The same thing is happening to my lady and her brigantine she bought.

@deadlykitten944
Trinkets require a specific place, e.g. large plants only go on the floor, those lights only go on the wall. Make sure you pick a place suitable for the trinket(s) you have.

Are they captain ships?