Skirts are hardly a deal breaker. They get in around the same range as pants, for women. Tight skirts like tight pants? Yeah, that’s going to restrict your body’s movement. Loose skirts? Those are fine. The high heels and sandals that usually come with them? That’s where it’ll fall apart.
You need proper ankle support, proper foot support, and proper knee support when you fight. This means fighting with a fully enclosed foot on a flat sole like a sneaker or not at all. (Trust me, you don’t want to be fighting barefoot anywhere other than on a mat unless you absolutely have to.)
The other problem with skirts is the same one you’ll get with shorts and short sleeve tops: lack of leg protection and skin protection. This equates to more injuries when falling (even on grass, but especially on asphalt), more friction burns, more bloody scrapes, and showing more scars.
It doesn’t matter how badass your character is. If she fights, she’ll get hurt. Training doesn’t make you super-humanly resistant to injuries, even if the injuries aren’t serious, she’ll be walking away with fights and training exercises full of little bumps and bruises. In terms of long term preservation, the skirts are impractical in the same way wearing skinny jeans is impractical. They don’t help you and serious combatants aren’t going to pick them as combat wear. Avoiding injury is important and that includes wearing clothes that help safeguard your body from injury. If your character is picking skirts as her preferred choice to fight in then you’ve got a problem.
If she’s in a situation where she could be in combat at any time, you might want to step back and think it through. “Badassery” isn’t really about how well your character wields a gun or a knife, or how “kickass”
they are. It’s how well they can sell that they know what they’re doing.
A character who chooses to ignore the reality of their situation, who
fails to come with the appropriate mindset, and dressed for their job
isn’t a badass. You wouldn’t go fight a fire in a skirt, you wouldn’t muck out a stall in high heels, you wouldn’t go wading through a sewer in your sandals, so why insist on fighting in skirt? Are you feeling insecure about this character’s feminity? Do you feel like you need to remind your audience that she’s female? If so, then in the words of Henry Jones: “Indiana, let it go.” Come to terms with the idea that women dressing appropriately for their job isn’t “dressing like a man”. Men don’t dress the way they do for combat because it looks cool, they dress that way because it makes sense.
If it’s casual wear or “civvies”, it really doesn’t matter.
So, what it really comes down to is a question of vanity.
Does this character mind other people seeing her bruises? Her injuries? Her wounds? Her scrapes? Her scars? Preferentially wearing skirts into a fight is a fast track to getting more of those than she might normally. Is it a problem for her? Is her appearance, in a conventional femininity way, something that matters to her? Do the opinions of others on the subject matter? Are her “looks” (again, in a conventional femininity way) something she wants to preserve?
For the record, it can go both ways. Some women are very proud of their bruises, proud of their scrapes, proud of their cuts and their scars because they can point to them and say “Hey! Look at this! This is mine! I earned this!” in the manner of “you should see the other guy!”. They love showing them off, even wearing clothes that expose them (and sometimes make other people feel uncomfortable just from looking at it). Other women? They don’t like it, they don’t want other people to see their injuries. It’s not a part of themselves they want to draw attention to. Whether it’s because they’re embarrassed or just don’t want to deal with the invasive questions, the stares, or the assumptions that someone is abusing them is up to them.
Both approaches, and all the myriad in between, are valid. Whether your character is perfectly happy to put on a miniskirt and tube top and go dancing with a body that’s black and blue, or moans, complains, and tries to conceal each new unnoticed scrape and bruise, it’s all water under the bridge.
What you should think about is how she deals with it and how she feels about it. In the end, whether you’re male or female, dealing with the physical fallout is part of combat. It’s actually part of all physical activities. It’s also what makes her human.