There are plenty of reasons to weaken a class after character creation. If the character is not working out, if it is to powerful for the rest of the PCs if it was allowed in with the stipulation that it might be revisited later.
So it is not necessarily bad DMing.
The DM should talk to the player share their concerns and see if the two can work on away to fix it so that both are satisfied. If they can't then the DM should allow a new character brought in with the same XP, wealth and magic items.
In a perfect world the DM does make sure he has everything discussed ahead of time. But DMs are human too and maybe he didn't think about how he was handling rests until they came up. It was the first session they are not so far invested in the game that it it will have that big of an impact.
Generally I'm the first to give people the benefit of the doubt, and with zero context is best to assume no malice nor incompetence, just regular human nature. But roll20 isn't a zero context environment, it is way different from a home game. It is basically a marketplace, an open one, with lots of spaces to discuss a game before even starting one. Maybe is the 3e/4e eras thing, but in such an environment the default assumption is every game is subject to RAW unless noted, a lot of players request their access to a game with that in mind. As such any houserule short of emergency ban has to be made explicit in the game description and adjacent forum. Of course this is no rule, but it is good etiquette.
The DM either hadn't thought of the houserule before that point or he had. If he hadn't and just thought it in the spot, he should have been more open to feedback and discussion, I myself commonly contain from changing things on the fly, if I have an idea I want to consider the ramifications before telling it to the players, and I ask for their opinion.
Sometimes I make changes before starting a campaign, but they aren't just occurrences, and I communicate the changes to prospective players before they join.
Now if the DM in question hadn't considered if he wanted to dial short rests before, he should have waited to see if the default was serviceable or not, and asked at the end of the session how would the players feel with the houserule. (Because we so far lack guidelines for dialing short rests, and dialing them is a change to RAW which is one of the few things a bunch of strangers banding together to play can implicitly agree on.)
Wanting to take away a class ability the first time it is used isn't a good precedent either, it is a sign of a controlling and reactive DM.