The main distinction I see is that most of the codes from the O26 range specify a condition; weight gain, recurrent pregnancy loss, hypotension, etc.
The O99.89 code can be used if the provider specifies a condition that affects pregnancy, but doesn't have it's own code. However, O99.89 is specific to childbirth and the puerperium, so during labor and for approx. 6 weeks after birth. This would only be applicable for encounters specifically for labor, delivery, c-section, or aftercare. If they had a not-otherwise-specified condition in the gestation period, O26.89[x] would be appropriate, with the last digit determined by trimester.
Lastly if the provider just says "other pregnancy complications" or some equally vague language, O26.9[x] would be appropriate, again with the last digit determined by trimester.
Hope this helps. Take with a grain of salt, this is abstract advice, not specific to a case, yada yada, insert disclaimer language here.