Any idea why flyctl showing this message?

Error loading config While parsing config: yaml: control characters are not allowed
Error yaml: control characters are not allowed

Can you paste the entire command and output?

E:\dev\wagtail\deseeart>flyctl status
Error loading config While parsing config: yaml: control characters are not allowed
Error yaml: control characters are not allowed

That’s it, nothing else other than this. Can this happen if I’ve deployed way too many updates on my website ?

That error means your config file is corrupt. I’m not sure how that could happen, but if you remove the file at ~/.fly/config.yaml it should create a new one.