I've been using Lyx and an MIT Template that is available from the link below (also including a minimal example) to write my Formal Lab reports for my undergraduate Physics labs. I (and my tutors) have noticed arbitrary indentations and spacing occassionaly throughout my report when I use this template.
Here's an image of an extreme case from one of my lab reports:
I would upload put in the minimal example code provided by MIT, but I'm not too sure how to do it; my knowledge of Latex code is very small since I primarily use Lyx
Thanks in advance :)
Edit: If you need anything in particular that would help you figure out what the problem is (e.g. a Lyx file of my Lab report) then feel free to ask :)
Here's a Lyx File. Notice that once you remove the tables, the spacing disappears (but whenever they are there, the spacing between the Conclusion section and the following paragraph is very large).