When you open a link that opens in a new container, you loose the history that brought you to that link. Clicking a link actually opens a new tab and simultaneously closes your current one. Going backwards is now broken and you have to shift cmd t to go through all your recently closed tabs or dig through your history if you are a user who regularly uses back on a browser.
I also ran into a bug where infinite temporary containers would open until the browser finally crashed. The fix was removing the add on.
I don't have that enabled, even ctrl-clicking something opens in the same container for me. Not perfect in terms of privacy paranoia (my HN container gets cookies from sites I go from HN to, unless I take the effort to explicitly open in a different container) but it has never annoyed me.
