What me disturbs most is that you are not using styles:
- No Paragraph Styles
- No Character Styles
- No Object Styles
I suppose you don’t use the other styles neither.
It is very important to use these style to avoid production problems as you have. I cannot determine where your problems come from, but—don't feel offended—such problems occur only or at least mostly when people are working without styles and are not using the guides given from the Master page. This indicates not a clean workflow. I think you should go back and start again with properly build up and correctly named styles, layers and masters.