Salem

I placed my boat in the mine, placed a crate full of ore in it, and now it wont let me take out the crate or lift the boat. I tried right clicking it in several different positions, and also lifting it.

When a canoe is placed on land, it is upside down. You cannot retrieve items stored in a canoe unless it is right-side up on the water, since otherwise they will be hidden from view and not clickable.

So I just cant get it back?

you just have to put it into water, then you can get your ore.

I cant lift it at all. Thats the thing.

Try destroying it, should get you your ore back, if not the canoe.

there is a way to take the crate back and not destroy canoe, I'll do screenshots later

if you turn the camera as shown on the screenshot you'll see small part of the bag that in canoe, try to click it and you'll take it back

Have you tried turning it off and then back on again?

relog. then dig next to the canoe until you can see the object inside using freestyle cam.