I'm circling back on this issue (https://github.com/dsifford/academic-bloggers-toolkit/issues/161) though I thought it had been cleared up, but I've retested my original post. Perhaps we hadn't tested it well enough originally, or something has changed in the erstwhile to change the behavior?

In any case, here's what I'm seeing presently (with the latest Version 4.7.2, WP 4.6.1):
Books with the same title, but different authors and different other meta data can be input, but when actually inserting the citation, the superscript number for the first book input with that matching book title is appearing.

The desired book reference does (now) appear in the list of references (it wasn't before), but appears under the subsection "Uncited items". This seems like the best/most intuitive way to display it from a UI perspective.

Example:
http://boffosocko.com/2016/07/25/introduction-to-complex-analysis-ucla-extension/

Several of these books have the same title, namely "Complex Analysis".
Most show up improperly when cited as 3 (the first one I input), while incomprehensibly to me, 6 and 8 show up properly instead of as 3 as the others do that have the same title. 8 and 9 on the last book at the bottom both appear properly though 9 has a longer title which differentiates it from the other.