This is a known problem, see here, which arises due to the need for RevTeX to compile 3 times according to the discussion there.
You have to compile several (three) times, without deleting .toc or .aux file.
At the first time, the toc is created. In the second run, the toc is displayed, but not yet all spaces for numbers reserved since they are now calculated and written to .toc or .aux, at the third time all is printed with correct placement and spacing.
How can we tell Lyx (pdflatex) to either compile this 3 times or maybe we can add the correct spacing in the preamble somehow?
I have been looking at Lyx>Preferences>File Handling>Converters and File Formats, but can't seem to figure it out.
I am using document class RevTex 4.1