index.php in output HTML - channel pages is there are anything to do to delete index.php from output html? This is not very "clear"... 

In my case its channel array and I call {{entry.url}}...
Any idea how could be this fixed / avoid?

Big TNX for any idea!
I'd suggest starting with the official docs on removing index.php from your URLS:

https://craftcms.com/support/remove-index.php

https://craftcms.com/support/why-index.php

And if that doesn't help, there are lots more environment-specific things here on Craft SE, you can check.