One involves ShotSpotter, the other Chicago Public Schools CEO Pedro Martinez.
The mayor has found himself on the rebuking end of a 33-14 vote last week by councilmembers who wanted to keep ShotSpotter, whose contract Johnson canceled. His recent push to oust Maritnez has created another battle with alders.
"He hasn't learned how to collaborate with, not only his colleagues, but even some of the folks who may not agree with them," said ABC7 Political Analyst Laura Washington. "Politics is a game of addition, not subtraction, and he's losing allies rather than gaining them."
A host of political observers blame the problems on the mayor's lack of political experience.
"There's a big difference between campaigning and governing, and a lot of new politicians don't understand that," said political consultant DelMarie Cobb.
Johnson is applauded for sticking to the agenda that got hm elected, but political analysts say he needs to learn to pick his battles and count his votes first.
The recent battles with city council also do not come at a good time for the mayor as he approached budget season, in which he will need broad aldermanic support to deal with a budget deficit approaching nearly $1 billion.
"He's burned up a lot of political capital; the same political capital, the same friends he's going to need to get through this budget," Washington said. "He needs votes, he needs to make friends, and he's made a lot of enemies that he's going to now have to go back to and woo, and that doesn't put him in a very good position."
Last week, Mayor Johnson said he's not worried about budget negotiations, and one of his deputy mayors stressed Wednesday that he is all about collaboration.
"We're not at war with city council. We've never been at war with city council. City council are great partners. We're going to continue to work with them on everything that is in their agenda and our agenda to work together," said Deputy Mayor for Community Safety Garien Gatewood.
Others said political battles at City Hall are not always a bad thing.
"But you also don't want to go from that fight right into another fight, right into another fight, all the way to the end, because eventually they're going to take a toll, not only on you but also on your reputation and your credibility," Cobb said.