Jones was perceived to have criticised Lohan in a tweet posted on the same day that Lohan was allegedly late to film her guest spot on Glee.
"Gonna be a long day!! Some ppl show up late and just throw a wrench in things. Not cool! I'd rather be an hour early (I was) than 5 minutes late," the actress wrote on Twitter.
Lohan's publicist later insisted that the Mean Girls star was on time for her Glee shoot.
Jones has now told Access Hollywood that her tweet was not written in reference to Lohan.
"It had nothing to do with her," Jones declared. "In a nutshell, I got to work early. And I said, 'Do you want me to go to hair and make-up?' I was an hour early, 'cause you never know with traffic and so they said, 'Oh no, there's some people late and blah, blah, blah'. So I'm like, 'Oh, God'."
She continued: "So I went to my trailer, started watching TV. I was reading tweets, and I said, 'Oh, it's gonna be long day, some people are late, throws a wrench in the day, extends everybody'. I had no idea who it was and it turned into a crap storm."
Jones added that she has nothing but respect for Lohan, who will appear as herself on Glee's season finale.
"I love her. I had no idea who it was and it really pisses me off that the snakes that got a hold of that and turned it into some BS that it wasn't," she said, adding: "That's not my deal."
Glee airs Tuesdays at 8/7c on Fox.