app-misc/beagle 0.2.5 removes a workaround for a memory bug in mono. It removes this because it causes thread safety issues. The memory bug is fixed in >=mono-1.1.13.5. So beagle 0.2.5 should depend on >=mono-1.1.13.5. Users are experiencing memory bloat because of this.
Related mono upgrade bug. BTW, seems that copying mono 1.1.13.4 to 1.1.13.6 works. Although 1.1.14 would probably be better.
I don't maintain mono. I've already answer you on dashbard-hackers ml. Beagle needs at least 1.1.10 version. It doesn't require 1.1.13.5 at all. Open a bug assigned to dotnet herd to bump mono.