Whenever I'm looking at Japanese there are times where I notice the れる conjugation is cut off. As an example, instead of する turning into される, it changes to されて. From what I know, れる is a past tense so される would be to have done. What does replacing る with て add here? It can't be a gerund considering it is already past tense, and I'm unsure using a request in past tense is appropriate either. Am I looking at this completely wrong?
You have a number of misconceptions here.
The ～て form is not a gerund, for one thing. It has a number of uses, but the main one is either connecting clauses. 「夕ご飯を食べて、寝た」 'I ate dinner, and went to bed' or connecting a verb to an auxiliary verb 「朝ご飯を食べてください」 'Please eat your breakfast'.
～（ら）れる has two uses, sort of. One is the potential form, expressing abilities. 「アレルギーでリンゴは食べられない」 'I can't eat apples, due to allergies', while the other is passive, which means that the subject of the verb is what is being acted upon. 「魚は猫に食べられた」 'The fish was eaten by a cat.'
Now, for ichidan verbs such as 食べる, these forms are identical, but for a godan verb, the passive form replaces the ending -u with -a and adds -reru, while the potential form replacing the ending -u with -e and adds -ru. So 話す has 話せる and 話される. Additionally する is an irregular verb with the passive される and potential できる.
Thus, ～されて might be 'was [some verb]ed, and', or it could form a request like 「騙されないでください！」'Don't be fooled!' There's no contradiction in logic here.