No, they have expressed concern over how the FCC plans to evaluate "harm," specifically with how seven rules for harm will be defined so that adequate legal challenges to them -- one way or the other -- might be brought. They're afraid they might be ambiguous.
However, overall they, like what the FCC is proposing.
[I]t appears that many of the proposed rules will make sense for the Internet. Based on what we know so far, however, the general conduct proposal may not.
To say that such concerns constitute "serious issues with the vast extent of the FCC's net neutrality rules" is hyperbolic.
Furthermore, if you read the ex parte letter linked, the EFF actually suggests additional regulation by considering what unbundling rules "might be appropriate for the 21st century, in a separate proceeding." If the EFF is so concerned about the "vast extent" of these new rules, why would they also be asking for additional rules?