I found the answer here: http://john.regehr.org/latex/. Excerpt:
When a non-sentence-ending period is to be followed by a space, the space must be an explicit blank.
So the second example should be:
After brushing teeth etc.\ I went to bed.
The converse of this problem happens when a capital letter precedes a sentence-ending period in the input, as in the first example.
In this case LaTeX assumes that the period terminates an abbreviation and follows it with inter-word space rather than inter-sentence space.
The fix is to put “\@” before the period.
So the first example should be
I watched Superman III\@. Then I went home.
A handy way to find this error is:
grep '[A-Z]\.' *.tex