I have my hotbar set up to have dirt on it with normal sorting, but currently I'm building something out of netherbrick and I put the netherbrick where the dirt usually is. When the netherbrick runs out it gets replaced with dirt. Not sure if this is intentional or not, but if it is how would I work around this?

If you have a rule setup to place dirt in that slot normally, the autorefill considers those as well as an additional 'what was last there' rule, and tends to pick whichever one matches first. It tends to prefer the default rules, although it more strongly prefers the most damaged tool or the smallest stack.