The Waqf signs (U+06D6 - U+06DC) do not combine with the previous letter if the preceding character is U+06DF (small high rounded zero) or U+06E2 (small high meem isolated form).
The problem is specific to MS Word 365 (latest English version). Browsers show the signs correctly.
The small high rounded zero looks identical to Arabic Sukun, except that it doesn’t change its form based on language. Functionally, it indicates a silent letter in Quranic typography, while the Sukun indicates lack of vowel.
Ideally, the Waqf signs should be placed a little towards the left of the last letter, not directly above it. Otherwise they distort the word by mixing with previous marks.