Out of curiosity: Why didn't Letsencrypt applied for a trademark right at the start? That this happens was quite foreseeable and occurs quite often if people forget to secure trademarks (I know this won't be a popular opinion because most as I like Letsencrypt and their outstanding service)
It costs $375 (plus lawyers fees, usually) and I suspect that they just didn't think it was necessary. Lots of organizations haven't and don't bother registering, unless they expect a problem. Lots of volunteer-run software projects have better things to spend money on and just never get around to registering their name as a trademark until someone else tries to steal it out from under them.
EDIT: For example, they probably spent a employee/retained-attorney time worth more than $375 just to put together their Trademark Policy page. [1]