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This is alarmist, and while technically true, shouldn't be an issue under normal brewing conditions. If you leave your wort out for several days after the boil before pitching and sealing it up, then yes, this it's possible to pick up contaminants and have them gain a foothold. But if you're boiling, transferring, and then aerating/pitching right away, it won't be a problem.
If the carboy, or if you're using a plastic funnel that isn't clean and sanitary, that's more likely your issue if it sticks around.
I would look to your bottling bucket spigot. You need to take it apart fully and clean it every single time. There's lots of little nooks and crannies inside that spigot where bugs can hide, and if a speck of wort or beer remains after you rinse it out when you're done, then the bad guys can grow in there.
Also, are you cleaning before you sanitize? Cleaning and sanitizing are not the same thing, and Star-San is a sanitizer, not a cleaner. If there's any soil whatsoever in your equipment (even if you can't see it), then Star-San will not be effective.
^ This +1. There are too many who use plastic and similar process without issue -- my simple scientist brain says if it were bad process, more folks would be suffering. Therefore I second the cleaning/sanitizing. Clean after using. Clean before using. Sanitize before and during using (StarSan sanitizes only while wet, if it dries, it isn't sanitizing). Bottle trees (if used), spigots, spoons, everything must be cleaned and sanitized.