Question regarding the Shaper Tool in Illustrator

Hi there. I'm currently making symmetrical items in Illustrator using the reflect tool (essentially creating half of custom shapes and making them perfectly symmetrical using the reflect and copy and paste tool), and making smaller shapes within the using the pen and shaper tool. 

It sounded and seemed simple in theory, but what happened in practice was that, particularly for more complex (especially curved) shapes, I ended up crating not only shapes that have many anchor points, but also jagged and random lines. At times, although there are two shapes recognized by the shaper tool (they turn grey when I hover the curser over them after selecting them and then selecting the shaper tool), they sometimes do not merge into a single shape (remaining two distinct shapes). 

What basically results is a mess of multiple anchor points, many lines created at random, and unnecessarily long amounts of time utilized cleaning up said mess (in addition to myriad anchor points unnecessarily increasing file size).

I was wondering if anyone in the Adobe community can advise on using the shaper tool efficiently.