After updating to Yosemite 10.10.2 on my MacBook Pro, InDesign is not displaying properly on my Thunderbolt monitor. When I open a file and move it over to the thunderbolt monitor, the window goes up into the top navigation bar, making the maximize/minimize/close buttons inaccessible. Also, when I bring up an action window, such as Open File, the window is half embedded into the top of the screen, making them unusable.
Been reported several times.
You might want to report it to Apple.