So let's take this circuit:
To find voltage across \$ V_1 \$, you do KVL in loop 1 to find \$ V_1 \$
\$ 5V + V_1 + V_3 = 0 \$
correct? But why is it assumed that current flows through the 5V supply? Aren't the positive and negative terminals of the battery (5V supply in this case) separated? Current direction defined as flowing from the positive terminal to negative terminal, but let's ignore that, and talk about what happens in reality. Physically, electrons will go from the negative terminal of the 5V supply around the loop to the positive terminal of 5V supply.
So, the 5V supply is really an open circuit, isn't it? Whenever you do KVL or these loop equations, why is it assumed that current flows seamlessly between voltage supplies?