Guaranteed buzzkill

Some other considerations...

When you built it in wood, did you already place the turret on there? Did you stand on there while the turret was on there? If not, did it collapse when you were standing on it as cobblestone or when the turret was placed when cobblestone? The added weight of the turret and/or you may have been the cause of the collapse rather than actually the upgrading.

One other possibility, though I've never experienced it and can't say if it even is a possibility, is that there might have been some lag (network lag, for example) as you upgraded the block and that caused a loss of stability due to loading lag or something.
 
Suggestion:
Next time you build, place simple plywood blocks below whatever you need to upgrade and remove them afterwards.
It should avoid the bug (if it's a bug) and it just takes a little bit more of your time.
 
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