Is it permissible to demand that the institution pay treatment costs based on invoices, knowing that one of the parties may demand that the institution disburse a treatment allowance?

It has already been explained to you that you are suffering from waswas (obsessive whispering), and you must reject it and not give in to it. You are not responsible if the pharmacist defrauded the institution and took the price of the medication again, for you have done what you could. You can warn the institution about this so that what is in your heart may be removed. The sin falls upon the one who committed the fraud, not upon you. Leave the waswas, seek refuge in Allah, and maintain your adhkar (remembrance of Allah) and du'a (supplications).