How can current be in different phases in the same wire at the same time?
Consider this: -

(http://stades.co.uk/index.html#transformers)

The two currents that flow through Rc and Lm are 90 degrees apart because one is a resistive loss (Rc) and one is the magnetization inductance Lm. The sum of those two currents does of course flow into the transformer primary terminals.