They are trying to get him for running a "crypto" service while Telegram doesn't even have end to end encryption!?
You can be pretty sure other apps like Signal and Whatsapp (with E2EE) have backdoors.
It's multilayer. To start with, Telegram is a honeypot. They do make false claims about their security features. They do have undocumented API calls of surveillance nature, some of these have been discovered and reported by infosec community. They allegedly provide privileged API access to RU security service and there are confirmed cases of FSB acquiring full data of deleted TG accounts. Yes, they do store data forever and there's no way for a user to delete it. Thus, valuable asset for any government. Obviously has nothing to do with true freedom of speech.