It's not a question of legitimate complaint. They didn't complain, they froze assets and halted the organisation's activity.
The question is whether or not the Indian government's actions are legitimate, and whether or not their stated reasons are true. On the later, it seems to be a clear no.
There were certain documents that shoud have been filed, but in general the interpretation or norm was that they didnt need to be.
The new govt which came into power eforced this rule and of course, everyone struggled to fill it - the media scoop was "non compliance".
IN addition, this was all done on the backs of a terrible IB (intelligence bureau) report which was leaked.
The report was used as an excuse to demonize NGOs and reduce any statue they had in the market of ideas.
I have read the report, and it is so laughably bad, that I wouldn't doubt if someone told me that all of India's security apparatuses had been compromised and were run by foreign powers.
Sections of that document included parts which warned that NGOs had been able to plot, on a map, the location of extant, proposed and in construction nuclear power plants. "The use of handwritten notes was to foil the ability of text scanners."
Additionally, there are multiple sections that correlate receipt of foreign funds as signs of collusion with foreign powers. Even if it is Greenpeace getting funding from international members.
The amount of actual scrutiny in 2014 on this document was nil.
If anyone reads it, you will immediately see what is up, since the sight of a google map with pins being lauded as a villainous mastermind about to damage India was laughable.
The question is whether or not the Indian government's actions are legitimate, and whether or not their stated reasons are true. On the later, it seems to be a clear no.