First Priest give flowers to devotee. After Puja is over and priest collect Flowers with money from devotee. Why so?
This practice is not a good one.It is started by some people with the need (or greed) of money.
The puja done here is Mantra Pushpam (Taittiriya Aranyaka Prapathaka 1, Anuvaka 22 Mantras 1-10). In many temples, priests chant this at the end of the puja.
The flowers are given to the devotees and the mantra pushpam is chanted. After completion of the recital, they are taken back and put at the feet of the god again. There is no involvement of money to the priest or anyone. Generally, people give some money has a dakshina to the priest for conducting puja. This later happened as a habit of giving money obligatory. he situation you have encountered is a distortion of a practice of voluntary dakshina given to the priest for conducting pooja for our welfare.