I found it an odd thing to say about an onging investigation.
Our system works on the idea that people are innocent. Prosecutors generally shouldn't make public declarations that a suspect is guilty.
Not that they don't do it, mind you.
It would be odd if a prosecutor, commenting on Mr X, accused of bank fraud, said in public:
"If we had confidence that Mr X did not commit a crime, we would have said so."
I think such a statement would seriously jeopardize the case against Mr X.
The only thing i can think of is that Mueller knows there's no case against Trump, and wanted to get a shot in at Trump.
Because I think as a prosecutor, Mueller would not have wanted to make a possibly prejudicial statement about an ongoing proceeding.
Anyway, we've known all along that charging a sitting President is a job for Congress.