This seems to be intended, I've seen it occur multiple times. I think it's not a glitch, but rather a way to break up the visual surface so as to not have a potentially 'boring' span of 100% carbon-copy crates. As to how to avoid it? I am not yet certain, but I have taken to spacing out my crates in one block depressions, and then placing a trapdoor overtop; it gives the more uniform appearance, and I just work the trapdoor like a flap and interact with the crate as such.
Hrm, you should be able to commit the transaction. Do you have room in your inventory? Have you clicked the 'Buy/Sell' button repeatedly? Maybe toss in a good ol' save/disconnect/reboot game just for good measure. Hope I can help, and if not, hope it all gets smoothed out sooner than later
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PastaNipples's post in are crates suppose to change size when placed on different spaces? was marked as the answer