Actually, maybe not. There are some more impressive ones:
The Big Short (Released 12/11/2015): $28 million production budget, $133,346,506 WW Gross
10 Cloverfield Lane (Released 3/11/16): $15 million production budget, $108,286,421 WW Gross
Daddy's Home (Released 12/25/2015): $69 million production budget (wat), $240,360,392 WW Gross
Overall, according to Box Office Mojo, their total box office numbers this year ($650.4 million) are up from last year ($575.9 million), but stuff like Ben Hur (which shouldn't have even been made yet cost $100 million/grossed $94 million), Zoolander 2 (which somehow cost $50 million/grossed $55 million) and Whisky Tango Foxtrot ($35 million budget/$23 million gross) really hurt them. Without those, I don't think the disappointing box office performances of Star Trek and TMNT would have been as damaging for them.
I also can't help but wonder if Star Trek's budget includes whatever they had to pay Orci and the original writers before they were removed from the project.
Edit: Watching the BTS stuff on Beyond and pretty much all of Yorktown was shot on location in Dubai, and a lot of the sound stage stuff was shot there too. I imagine that's pretty expensive. I guess Justin Lin wanted to do as much location shooting as possible so they built a lot of outdoor sets (i.e. the rock quarry is one massive outdoor set built in an actual quarry). Just from the BTS on this movie, it looks really expensive.