Spacing in the presence of sub and superscripts

[KenyC]

\begin{aligned}
\frac{dq_{AB}}{dt} &= \left( r_E^2 S + c_{AB}\sigma^2 S_\eta\right)q_0 + S_F\epsilon q_{AB} + S_B \epsilon \left(1-p_0\right)\left(q_{AB}+p_0p_{AB}\right) \\
&\;\;\; + S_C \epsilon^2 q_0\left(2\kappa p_{AA}p_{AB}+\left(N_E-2\kappa \right)p_{AB}^2\right) + S_C^I \epsilon^2q_0N_Ip_{EI}^2
\end{aligned}

Renders as:

Letters with subscript and superscript are too close to their neighbours causing some overlaps

[KenyC]

On a more minimalistic example:

S_C \epsilon

Renders as:

LaTeX, on the other hand, successfully avoids the overlap: