Here are some possibilities.
1. A lack of money. Superheroics can result in injuries, but anybody with a secret identity probably wouldn’t want to reveal those injuries to an insurance company. (Otherwise, they’d need to lie to the insurance company or reveal their secret identity). Second, a lot of superheroes spend what must be substantial amounts of money on their superheroics. For example, Peter Parker is practically on the verge of starvation (and has been evicted at least once), but he’s still buying high-grade flame-retardant fabric for costumes. Even a wealthier team like the Fantastic Four could have financial difficulties sometimes. Their headquarter alone would probably cost hundreds of millions of dollars a year (in financing/interest, property taxes, maintenance, insurance to protect nearby buildings from FF science, building upgrades, etc). Government agencies might face budgetary restrictions, particularly if they’ve antagonized Congress/Parliament.
1.1. Troubles at work and/or school. Superheroes don’t have very much control over when supervillains attack, so they frequently have trouble maintaining a regular work schedule. Superheroes can take some steps to minimize the damage to their day jobs, but a worker that’s frequently late and/or absent without leave will probably get in trouble with his/her boss and/or school.
2. Physical stresses of a highly dangerous job. For example, injuries stemming from fights or overexertion, a lack of sleep and/or time to recuperate, exposure to highly dangerous chemicals or alien symbiotes, mild aging (Batman’s at least in his 40s), etc.
2.1. Mental stress and/or combat fatigue.
3. Pressure from friends/family/loved ones to give up or minimize superheroic activities. They may be concerned about the superhero’s well-being because it’s such a dangerous job and/or the superhero might not be well-suited for the job. Alternately, a spouse or lover may feel that the toll on their relationship is getting too high, particularly if he/she has been kidnapped or nearly killed before.
4. Disagreements with other protagonists (superpowered or otherwise). For example, Lucius parted ways with Batman over philosophical differences. Superheroes might privately and/or publicly hold each other accountable if a mission goes awry. Alternately, if there’s a crime or disaster where multiple superhero groups respond, the groups might have trouble cooperating–the teams might be very different philosophically, tactically, demographically, etc. If a super-SWAT team and a team of superpowered high school students both respond to a hostage crisis, there are a variety of reasons the SWAT commandos would not want to trust the students with any responsibility. Peter Parker is good at many things, but he’s not extremely methodical and probably doesn’t have much experience with hostage situations. Alternately, the high school students might have trouble cooperating with the SWAT team, if they’re convinced that the SWAT team is so gung-ho they’re going to get a lot of hostages killed and/or the SWAT commandos don’t have the right superpowers for this situation and/or are using a more standard set of strategies against a completely unpredictable adversary.