– This is extremely rare, and can only occur on a temporary basis. Are you absolutely sure that (1) the spouse is non-resident at any time, and/or (2) non-resident the whole of 2015? - Recent immigrant-in-process? - Tax Treaties? (In particular, caution regarding section 250(5) considerations regarding the taxpayer). Maybe the taxpayer him/herself isn’t actually tax resident in Canada? This family’s tax situation sounds like it could potentially be quite complex.
“However, the warning still come out asking me to select the spouse net income is 0. How should I fix this? If I enter an income for the spouse, it will be used toward the calculation of the GST credit, which shouldn’t happen.”
– where there is a spouse, you cannot just decide to omit their income… There are a whole lot of income tax act sections that depend upon the income of the spouse being taken into consideration in the calculation…
In particular, on the facts you have outlined, IF the taxpayer is tax-resident in Canada, then your assumption about income for GST credit would appear to contravene requirements of section 122.5 of the act for Income inclusion, and also the spouse does not sound like a qualified relation with respect to the Credit?