Earlier today I tried to use the Shovel to bypass Union Cave (I had already walked through it). When I tried to use the burrow, it asked me for a Pokemon with Dig - I currently do not have one and was under the impression that having a Shovel would allow me to bypass that.

 

For comparison, the Shovel had worked properly for every cave I tried in Kanto after putting my Dig Pokemon in storage.

 

Am I missing something or is that a bug?

It might depend on the amount of badges you have in Johto, because if you had no badges and you were able to use dig (or had just three or four badges) anywhere in Johto, you could dig from Violet to Blackthorn via Dark Cave without any badges and go straight to the last gym badge skipping all of the region's story.

 

It might be possible that this restriction applies until you've successfully obtained enough badges, but if I were you I'd wait until a content scripter answered your post :)

Digging from Violet to Blackthorn that early wouldn't work since I would have had to see both sides of that cave.

 

My issue is that I've gone through Union Cave, but still needed a Pokemon with Dig.

 

At the moment, though, it seems that problem has gone away but I want to be sure I'm not missing anything.