Restricted Mode aims to filter out "more mature content" and is switched off by default.
But some vloggers, including Tyler Oakley, say they're "perplexed" by non-explicit material being blocked.
The site tweeted: "We regret any confusion this has caused and are looking into your concerns."
YouTube said: "LGBTQ+ videos are available in Restricted Mode, but videos that discuss more sensitive subjects may not be.