Because both sets of people were treated exactly the same by the system. I.e. inhumanely.
FYI, they didn't lose the paperwork.
UK gov destroyed the paperwork, then deemed people to be illegal migrants.
Then those people were told: quit your job (or we'll force it), leave your spouse, move out of your home, and leave the country. Have 2 weeks notice because we're nice. Obviously with nowhere to go to. And because married people do not have the right to residency, if they were married to a UK citizen that didn't protect them either.
And then consequences started to happen for real. They couldn't just ignore these notices. Jobs were lost. Money was stopped.
As I said, one person even died due to life-critical hospital treatment withheld, and I'm sure many others were pretty worried because all of them would have been denied medical care until the case was settled, and lost their incomes. A number of them were illegally deported.
UK gov has done similar things to other people, not just the Windrush crowd. But Windrush got the press because it was more people at once and older people. There are others who have done everything correctly, paperwork, fees and all, and have kept their own copies of paperwork to confirm their status is fine. Who have then been told, surprise!, quit your job, ditch the tenancy, leave with 2 weeks notice etc.
As it happens, the UK has plenty of people in it who believe they are legally resident and one day find out they are not on some unknowable technicality. And others who are in fact legally resident but the Home Office decided to kick them out anyway.
For a example a number of EU citizen students found out they were not eligible to remain in the UK because they didn't purchase some kind of private health insurance - a condition nobody knew about, nobody was told about, and the Home Office was unable to explain, other than to say they should have purchased it when they arrived as students so that's the reason for telling them to leave.
That kind of technicality. Note that nobody else had to buy this mythical insurance, only students, who weren't told. Essentially the Home Office looks for loopholes to catch people in, that nobody reasonable knows about or would try to enforce. Unlike other areas of law, where "what is reasonable" is taken into account in a principled way, and a process of restoring balance takes place if something is a bit off, the Home Office seems to lack this aspect, perhaps in its pursuit of quotas for kicking out X people a year without regard for whether it's the right people, or even the people intended by policy.
As you can imagine some of these cases end up in court because it's the government breaking the law. But the court system is not well suited to protecting the individuals in these cases, and people can't afford the legal fees.
You often need a judicial review (which is very expensive), because the ordinary policy is "deport first appeal later" or "no appeal possible" depending on the case. Under "deport first appeal later", people usually fail to appeal even when they would win, because it's highly impractical when you can't access your own documents from abroad any more; yet if they do appeal, most appeals are won because the government is found to be not following the law.