It may always happen but it would happen less if we updated patent laws to fine people who filed invalid patents or enforced some kind of similar punishment. If you file a patent, it's up to you to verify that your patent is actually valid, and the courts shouldn't have to do that legwork for you. It also doesn't help that the patent office/components of governments don't review patents as thoroughly as they used to. Same with trademarks.
I generally don't like the current patent law but it sounds a bit off to pay the government & wait for them to review your patent claim and then get fined by the government when both of you were wrong about it. There are already processes to additionally fine a company bringing about a truly frivolous patent lawsuit, it's just rare because usually it's not so cut and dry as we'd like it to be.
I mean my idea isn't the only one in that solution space. My reasoning was to ensure that the government actually reviewed the patent and ensured it was valid instead of rubber stamping it. Or, even better, the filer of the patent application would do that. Although the best is probably to make software unpatentable anyway.
> In the 1980s, when IBM accused Sun of violating seven patents, Sun examined the patents and argued that IBM didn't have a case. The reply of IBM's lawyers was "maybe you don't infringe these seven patents. But we have 10,000 U.S. patents. Do you really want us to go back to Armonk [IBM headquarters in New York] and find seven patents you do infringe? Or do you want to make this easy and just pay us $20 million?" And Sun paid out.[4]