The referendums they held were boycotted by a huge majority of the population and due to the low turn out not considered valid. There is a VERY strong anti-statehood movement in puerto Rico and a minority that want full independence and a minority that want statehood.
The Puerto Rican government chose not to pursue statehood based on the low turn out, but the option is still available to them anytime. This has nothing to do with the USA federal government and everything to do with Puerto Rican politics.
It's important to note that more than a quarter of these votes were spoiled on the statehood question, so the democratic legitimacy of that portion of the vote is quite reasonable to question. The effective turnout would have been about 57%. Were the spoiled ballots to have been counted only 44% of people casting a vote would have favoured statehood.
Boycotting a vote is nonsense. If you want to have your voice heard, then vote. They were just trying to undermine the voting process because they knew they would lose.
The Puerto Rican government chose not to pursue statehood based on the low turn out, but the option is still available to them anytime. This has nothing to do with the USA federal government and everything to do with Puerto Rican politics.