There’s a recent change in the handling of SSH keys in MacOS Sierra that means you need to enter your passphrase each time a key is required. There’s an open Radar issue about it and it’s intended behaviour now.
You can work around it by implementing one of the solutions at the links below, I personally went with adding:
ssh-add -A 2>/dev/null;
into my .zshrc file and that solved it for me (or .bash_rc if you use bash).
More information and solutions can be found at: