During the battle between the Aurors and Grindelwald there is a moment when Grindelwald's attention is drawn to Leta. They have a brief conversation with Grindelwald asking Leta to join him. Leta then turns to the Scamander brothers and says:
I love you.
It is left unclear as to which one she spoke to but was there any evidence in the film that can give us an idea of which she was talking to? Perhaps there has been an interview dealing with this.
In the screenplay of Fantastic Beasts: The Crimes of Grindelwald, it’s said that Leta looks toward both Theseus and Newt when she says “I love you” and no further explanation is given.
She looks toward both THESEUS and NEWT, who are watching her, stunned.
LETA
I love you.
- Fantastic Beasts: The Crimes of Grindelwald (The Original Screenplay)
This could mean she loved them both, possibly in different ways - it can but doesn’t necessarily mean she was still in love with Newt while still planning to marry Theseus. It could mean she loved one of the brothers as a friend, and the other one romantically.
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).
