Question regarding the trigger circuit for an SCR-based coilgun
A SCR when triggered it conducts until the current through decreases to the value of less than holding current Ih. Bigger SCRs have also higher Ih, smaller SCRs have low Ih. 

Now what happens is that you trigger the SCR and when the caps are drained, the charging circuit still delivers the current which is higher that the Ih of your SCR.
You can increse the resistor value of R1 to limit that current.

R3 limits the gate current, so you might increase the value according to used SCR.