In my opinion, everything indicates that she was saying "I love you" to Newt.
When Newt and Leta met at the Ministry of Magic in London, Leta said "Theseus was disappointed you couldn't come to dinner any of the nights we've asked you." First, I wouldn't be surprised if it was her idea to keep inviting Newt for dinner (whether she asked Theseus directly to invite him, or as a smart woman, skillfully instilled such thought in his mind). Second, women, more often than men, are less direct when communicating their feelings. For Leta, it was easier to say "Theseus was disappointed" rather than "I was disappointed." Subsequent scenes further confirmed that Theseus could easily survive Newt's absence in his house.
"He's your brother, Newt. He likes spending time with you...and so do I." said Leta as they were heading toward the room where Newt had a meeting with several officials (including Theseus). Here, Leta made it more obvious to Newt that she is (still) in love with him. She also enjoyed talking about an incident that took place during their school times - talking about something that involved the two of them. When Newt saw his brother coming, he pretended not to remember the part when Leta set off a Dung bomb under the principal's desk just to be detained together with Newt to make it look like they were just making small talk.
I believe Leta agreed to marry Theseus only to be close to Newt. Again, people often do that in life (they either "coincidentally" become neighbors with people they secretly love, or they marry their family members).
Later on in the movie, Leta arrives at Hogwarts with Travers and other ministry officials but instead of going with them to interrogate Dumbledore, she goes straight to one of the classrooms where she lovingly caresses the L+N carved in a school desk.
In her last scene when she knows she is going to die, she finally decides to say what she really feels toward Newt.
Last but not least, the script says "she looks TOWARD" and not "she looks AT" which is a very big difference. I may look toward a group of girls but actually and intentionally look at one of them only (especially when they stand close to one another).