oh yeah I had that happen too, I was playing around with seating and riding - ended up freaking out
I didn't save - just went to either menu or desktop, can't remember, and reloaded back when I saved after resting (wasn't long before it happened)
as for the lids - yea, I see that is the case now. I must not have realized right away that I had shoved my lantern in the first crate and lidded it shut - Btw, You should get used to doing that, carrying your lantern in the crate, lidded - works as a basic "I can still see where the flip I'm going" light thx to the gaps in boards - and that way you ain't gotta choose between carrying ore and seeing.