Talks of sexual assault and death underneath, read at your own risk:
Did Frank Booth rape Jeffrey Beaumont?
Originally, Jeffrey had it much worse in the script. He would wake up the morning after he got abducted by Frank without his pants, with the words "FUCK YOU" written on his legs with red lipstick, making it very obvious that Frank raped him. The scene was rehearsed, as it can be heard fragments of it during "No Frank In Lumberton", as well as this photo of Kyle MacLachlan with David Lynch, Isabella Rossellini and (probably) Fred Carusso taken by Peter Braatz:
During production of Blue Velvet, Kyle MacLachlan was anxious (arriving to Wilmington a week or two before production started) and depressed because after the critical and financial fiasco that was Lynch's Dune, he couldn't get any jobs thus fell into an depression and had an existential crisis.
On top of that, his mother got diagnosed with cancer and objected to his involvement in the movie after he showed her the script (she died in early 1986, so she never saw the movie and it left Kyle devastated). He was in a very dark and sensible spot during the production, and begged Lynch to scrap the scene where the rape on Jeffrey was more obvious.
In fact, the scene where Jeffrey was crying is not Kyle MacLachlan acting. He was actually crying.
Regardless of it, Jeffrey's fate doesn't change much in the final cut. After Mike rear-ends Jeffrey's car after the dance, Jeffrey's first reaction is to yell: "It's Frank!". And when he goes to Dorothy's apartment for the last time and meets Frank in the stairs, Frank recognizes Jeffrey because of his "cute little butt."
Jeffrey's still a rape victim regardless because he also gets raped by Dorothy when he first meets her, no matter what "analists" or critics say.