Љ љ - Represents /ʎ/ in Serbian and Macedonian but represents /l/ here, because of the above.
Й й - Represents /j/ in Bulgarian, Russian, Belarusian and Ukrainian but represents /ɨ/ here. Ј ј was already used to represent /j/ as it was identical to the letter used in Polish Latin (J j) for the phoneme. Й й was chosen to represent /ɨ/ because of the similarity in pronunciation to the phoneme /i/ (presented by И и).
Ӂ ӂ - Represented /dʒ/ in Moldovan but represents /ʑ/ here. Џ џ was already used to represent /dʒ/ and there was no Cyrillic letter representing /ʑ/ (separately from /ʒ/ or /ʐ/). The phoneme /ʑ/ is similar to the phoneme /ʐ/ and so this is reflected here: Ӂ ӂ is similar to Ж ж.
Щ щ - Represents /ʃt/ in Bulgarian and /ʃtʃ/ in Ukrainian but represents /ɕ:/ in Russian and /ɕ/ here. There was no need to represent /ʃt/ and /ʃtʃ/ with one letter here and there was no Cyrillic letter representing /ɕ/ (separately from /ʃ/ or /ʂ/). As the phoneme /ɕ/ is similar to the phoneme /ʂ/, Щ щ was chosen because it is similar to Ш ш (coupled with the fact that Russian uses this letter for a lengthened /ɕ/ - /ɕ:/)