It seems the font used in the document does not support those characters. Install the Andada typeface (it has been designed for Guarani), set a test document to use it and try again.
EDIT: Diacritic positioning is managed by mark and mkmk OpenType tables. Most fonts define combining tilde (U+0303) combinations only for ‘n’ and vowels (ãẽñ, etc.) and Andada is no exception on that. In fact, it turns out that you cannot, at least, not easily, get a tilde on top of a g with Andada, but you can with another open source font called Allegreya: with it you can use the normal tilde ~ (U+007b) as combining mark for g and G, so it’s possible to use that to insert those characters. It also includes the “saltillo” Ꞌ as U+A78B (Latin Extended D block).
The same is valid for Alegreya Sans.
So, in conclusion: scratch the previous recommendation and use Alegreya, it’s a better typeface 
EDIT 2: For some reason, if you type the combining tilde Unicode code after the consonant and then press Alt X it works on most fonts, including Andada, even if some fonts put the diacritic in the wrong position due to a bad definition in the corresponding OpenType tables. For example, by typing
G0303
and then pressing Alt X you’ll get the G with tilde in Writer.