I really don't know what happened over there at Groupon: http://gnome.groupon.com/#intro/index Did they truly not know? Did they just think the Gnome project wouldn't care? That they'll win the lawsuit?
Trademarks aren’t universal; they are divided into classifications e.g. market segments. Just because the name is the same, doesn't mean the PTO will think of them as being in the same space.
- downloadable computer software for creating and managing a computer desktop
- downloadable computer software for use as a graphical user interface
- technical consulting services in the field of computer software
whereas the Groupon product is "a tablet based point of sale operating system for merchants to run their entire operation." Except I'm pretty sure they mean "operating system" in the plain-english sense, not the "computers" sense. Groupon could apparently avoid infringing in the goods categories by not making its PoS app downloadable, but it's hard to imagine it not infringing in the category "technical consulting services".
And yeah, going just from my own idiosyncratic views of the world... a PoS app for tablets does not differ significantly, in terms of what it is, from desktop software for PCs. Here's some coverage from 2012 of an effort to get GNOME software to run on android: http://lwn.net/Articles/510465/