/bin/ls output does not match manpage

The order is determined by the collation sequence of your locale.

Ex. in my default locale (which is en_CA.UTF-8)

$ ls -A1
a
.b
c

whereas in the C locale

$ LC_COLLATE=C ls -A1
.b
a
c

(I used -A instead of -a to eliminate the . and .. directories).

Another way to get the order you want might be to use the -v (version sort) option as suggested in Grouping hidden files and directories with ls - although that's not really what it is intended for:

  -v     natural sort of (version) numbers within text

Since ls is almost certainly already aliased inside your .bashrc file, you could simply modify the alias(es) there to include the -v.