Installing ASP.NET 1.1 with default parameters will set itself as the default framework. (ASP.NET 2.0 doesn't do this. It's more gentlemanly and doesn't change existing IIS sites without you telling it) Additionally if anyone runs aspnet_regiis /i on the server, that will set a particular framework as primary across the board. As squillman said, restoring from a previous backup could also change the framework versions (depending on what it was set at).
Hotfixes won't change things unexpectantly unless you run into some type of bug. I have seen issues with ASP.NET 3.5 SP1 causing issues on some servers. That has caused reverting back to v1.1. I haven't seen it occur on hotfixes or patches.