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.
"We are so proud to represent LGBTQ+ voices on our platform - they're a key part of YouTube what is all about."
Stonewall campaigns for the equality of lesbian, gay, bisexual and trans people across Britain and says young YouTube users often get useful information from the site.
A spokesperson said: "Classifying lesbian, gay, bi and trans content on its site as 'objectionable' sends a damaging message to all YouTube users.
"Restricting this content implies that LGBT issues cannot be 'family-friendly' or age appropriate, which is worrying, as young LGBT people often look online to source information and look for support from their peers."
How Restricted Mode works
The company hasn't addressed how Restricted Mode works, or why it's blocked certain LGBTQ videos, but the statement added: "The intention of Restricted Mode is to filter out mature content for the tiny subset of users who want a more limited experience."
Restricted Mode is intended to protect younger viewers from seeing adult content.
YouTube says it uses community flagging, age-restrictions and "other signals" to identify what is potentially inappropriate content and filter it out.
Is all LGBTQ+ considered 'inappropriate'?
Many LGBTQ+ YouTubers say that their videos are automatically flagged and hidden while in restricted view, even when the content isn't intended for older viewers.
Singers Tegan and Sara tweeted that some of their music videos had disappeared in this view, while SeaineLove, a transgender YouTuber, said her recent videos about her transition were blocked.
Rowan Ellis, who makes videos about pop culture from a feminist and LGBT perspective, made a video saying 40 of her videos are blocked in Restricted Mode.
"It's something that people are just starting to realise the extent of, particularly in regards to LGBT content.
"This is something that no-one is really sure how it's working.
"I think it's really important to look at why LGBT has been deemed as inappropriate."
British YouTuber Calum McSwiggan said that his video about how he came out to his grandmother, which was aimed at helping younger viewers, was hidden in Restricted Mode.