Can your Sophia credits be rejected when applying for a Master?

[allvia]

My plan was to study all the courses before paying for a (Sophia) subscription.

Sophia doesn't work that way.  It is not a pick a subject and take a single exam.  If you have the time to study a subject well enough to pass a general exam it is safe to say you have time to work through the Sophia courses.  I would have to agree that overall your budget for Sophia vs Saylor is likely equal to each other - Sophia will be easier to achieve.

As far as the credits being rejected when it comes to graduate programs - as others have already made the point that Sophia or other alternative credits are part of your degree as a whole. When it comes to graduate schools they look at the degree as a whole, not the individual courses.  An ideal example of "the whole is greater than the sum of its parts" (Aristotle).  

Don't confuse the schools you're inquiring on graduate programs for by asking specifically about ACE, Sophia, etc.  Ask if you graduate with a bachelor from an US RA (Regional Accreditation) school (such as TESU, SNHU, etc) and were able to meet many of the general education requirements through Pass/Fail methods will it impact your admittance? It is likely they'll tell you as long as you have a GPA based on X amount of credits, or your master degree program prerequisites must be graded, or maybe they'll just say that is fine.  You're too focused on the parts, not the whole. One thing we have learned on this forum over the years is that admission advisors, at nearly all schools, get confused when you're focused on something they know nothing (specifically) about.