Can an acrylic type retainers cause bad breath, flem, or sore throats?

Not likely: removing your acrylic retainer after eating and at night to rinse off or soak is very important and helpful in keeping bacteria from overpopulating on the acrylic. Bad breath can be a possibility if your not. In regard to the phlegm...the natural reflex of the mouth when food or anything else enters is to produce increased saliva. sore throats is most probably unrelated

Retainers/bad breath: May be associated if optimum oral/retainer hygiene not practiced. Brush teeth 2x/day for 2 full minutes. Floss daily. Brush retainers 2x/day w soft t'brush but do not use t'paste on retainers. Place retainers into Denture Cleaner daily, follow package instructions. If you do all of these steps and bad breath persists, see the Dentist or Orthodontist who made your retainers.