Been like that since release

I think at release you didn't have to upgrade it at all, but then first patch after yeah they changed it to the current way. I kind of forgot about it as I haven't being using fissures much, but it still seems weird.

Wasn't sure if this was an intended choice for this tower, kind of like how the archer towers can be spam built. But since they approved it, I guess it is an oversight not a design choice .

This will be changed after the Trials Update!

Now that the Trials update is here, I can confirm that this is fixed.  Fissure of Embermount require time to complete the upgrade process if upgraded during the Combat Phase.