That says a lot about your packaging hygine. With alien, you're essentially dumping the contents of an RPM on hosts it wasn't meant for. It doen't matter that you converted it to deb format along the way, it's the same if you actually install it.
Did you ever read a single line of alien source code? It extracts the metadata and files from a package, and re-archives it. That’s about it. It doesn’t handle package version differences, path differences, distro-specific rules, nothing. If your package has dependencies, forget about it because alien won’t retain dependency information it all. In other words, it only “works” for the most simple of cases.
I suggest you read the source code too, because otherwise you can cause real damage if you use it without understanding how it works.
That says allot about you packing hygiene, and you don't dump it..that you can do with tar alone. You convert it to a deb.