Sometimes it's because you need to support ancient esoteric hardware that's not supported by any other tools, or because you've built so much of your own tooling around a particular tool that it resembles application platform in it's own right.

Other times it's just because there are lots of other teams involved in validation, architecture, requirements and document management and for everyone except the developers, changing anything about your process is extra work for no benefit.

At one time I worked on a project with two compiler suites, two build systems, two source control systems and two CI systems all operating in parallel. In each case there was "officially approved safe system" and the "system we can actually get something done with".

We eventually got rid of the duplicate source control, but only because the central IT who hosted it declared it EOL and thus the non-development were forced, kicking and screaming to accept the the system the developers had been using unofficially for years.