Dan Gilroy tells TMZ he’s not upset over Shelley’s omission from the segment ... he's giving the Emmy producers the benefit of the doubt, saying it may have been an oversight -- noting segments like these are planned way in advance.

Dan also tells us, in the grand scheme of things, Shelley being left out of the segment is small potatoes compared to what he and Duvall dealt with over the past few years ... considering she suffered greatly while battling diabetes, which ultimately led to her death in July.

He actually watched the "In Memoriam" segment and thought it was great -- praising Jelly Roll’s terrific performance, as late icons such as Richard Simmons and Shannen Doherty were honored.

Dan tells Shelley’s fans he appreciates their support and knows their hearts are in the right place, but urges them not to get too worked up about her absence from last night's show ... because life’s too short.

Since Shelley died, Dan says the response from fans has been wonderful, with people calling and writing him to send their best wishes.