D3 Javascript Force Directed Graph

I have a D3.js force directed graph project that has 2 small bugs. I'd like to have these 2 bugs fixed. Bugs: -------- 1. Line is showing through circle. I'd like circle to show above lines. 2. The bug involves the order of removing circles. * Add gene => add pathway => add process => remove pathway The graph shows incorrect circles I've verified the objects in console, and the array has correct objects after I remove pathway but in D3 graph it shows incorrect circles. But if I add gene => add pathway => add process => remove process Then the graph is fine. Thanks for your time.