If your words are being h-yphenated, like this, with jus-t single letters at the beginning or the end of the word, you may have a version mismatch problem. TeX's hyphenation system changed between version 2.9 and 3.0, and macros written for use with version 2.9 can have this effect with a version 3.0 system. If you are using Plain TeX, make sure your plain.tex file has a version number which is at least 3.0, and rebuild your format. If you are using LaTeX 2.09 your best plan is to upgrade to LaTeX2e. If for some reason you can't, the last version of LaTeX 2.09 (released on 25 March 1992) is still available (for the time being at least) and ought to solve this problem.
If you're using LaTeX2e, the problem probably arises from your
hyphen.cfg file, which has to be created if you're using a
multi-lingual version.
A further source of oddity can derive from the 1995 release of Cork-encoded fonts, which introduced an alternative hyphen character. The LaTeX2e configuration files in the font release specified use of the alternative hyphen, and this could produce odd effects with words containing an explicit hyphen. The font configuration files in the December 1995 release of LaTeX2e do not use the alternative hyphen character, and therefore removed this source of problems; the solution, again, is to upgrade your LaTeX.