Am I supposed to be using Mixed Effects?
I always thought that the mixed effects model was for logistic regressions when my dependent variable was categorical

This is not true at all. We use mixed effects, in particular random intercepts when we have clustered data, such as repeated measures on individuals, or sampling within clusters such as schools, or regions, or countries. It is certainly not the only approach - instead we can use Generalised Esitmating Equations, or just fit fixed effects for the grouping variable, but when there are a large number of groups, and we can justifiably consider their &quot;effect&quot; to be normally distributed and uncorrelated with the residual error or the fixed effects, a mixed effects model is often very attractive.