Formatting Issues when editing

In the past few weeks, I have had issues editing PDF's. Now, this is something I do regularly but this issue has just started to happen.

I get multiple editing boxes overlaying each other, text and images, If i am editing text the text box may be overlapped with other text box/es.

They are sorted of layered but only part of each box is editable, therefore I really can't edit anything without mucking up the formatting of the whole document. These docs are produced by me in various programs ie word amongst others and saved as PDF's but when I need to edit to update etc it is a nightmare and virtually impossible. Any ideas??