I once interviewed somebody about this very topic and here's what they told me... #4 and #5 seem most relevant to your issue.
1) Because E.coli is known to live and multiply in ground beef, any chili recipe including ground beef should be cooked so that E. coli is killed....a minimum of 155°F, with 160° preferred.
2) It should be recalled that even though beans may start off dry, once water is added, they can easily become a "potentially hazardous" food, allowing harmful bacteria to multiply to levels that can make us ill.
3) Of all the things we do to foods, by far the leading cause of foodborne illness is improper cooling and reheating of leftovers. All leftovers (including chili) need to be cooled rapidly and not left to stand at room temperature to cool...in fact, in the temperature range of 40°–140°, bacteria can double their numbers every 20 minutes!!
4) When reheating, all leftovers must be reheated to an internal temperature of 165° (yes, even chili) in order to kill the bacteria that can live and multiply in leftover foods (usually clostridium perfringens).
5) Once a portion of a leftover has been reheated, any remainder of that portion must be discarded...we simply cannot safely reheat foods another time.
If you have food safety concerns, the Food and Drug Administration (FDA) operates a 24-hour hotline at (800) FDA-4010.