I am translating with poedit. However poedit seems to be ignoring apostrophes. For example shouldn't is coming through as shouldnt. I am encoding in utf-8. Does anyone know why this is the case and if there is a solution ?
You need to use the html entity: ’
Source: http://geektnt.com/tag/poedit
Some text characters need to be converted into html entities otherwise they will not display correctly. A very common example is a word containing an apostrophe or single quote (‘) which needs to be replaced with ’ — for example, Chloe O’Brian should be written as Chloe O’Brian. For a complete list of html entities, visit W3Schools.
I assure you that Poedit isn't somehow ignoring or eating apostrophes — that's preposterous. It's just an editor that puts whatever you wrote, exactly as you wrote it (yes, including ' or any Unicode characters), into your PO and MO files.
Your problem is in your PHP code where you incorrectly escape the (translated) strings before printing them — how and in what context you do that is unfortunately something you didn't share.
But this is why e.g. WordPress has functions like esc_attr_e that do any necessary escaping and do it correctly, so that you don't have to do anything ridiculous (and painful to work with!) like substituting ' with ’ in all your translations (which wouldn't even work when using untranslated text…).