This issue is similar to my report for [url=https://www.bungie.net/en/Forums/Post/264910462]K1 Logistics[/url]. Sometimes the first objective in Skywatch (secure three zones with goods) does not grant points. This can happen with any zone.
I've attached the Imgur post with an example, will add more if it happen again. The very clip shows a case with properly awarded points, 8501 in total which is equal 3500 (bonus) + 1667 (zone secured) * 3 (# of zones). The second clip shows a case when the last zone didn't grant 1667 points. I still got A score, because I killed Vanguard Wanted previously (bonus 1500 points).
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Hello there, Thank you very much for the detailed report. I'm sorry to hear that you sometimes have issues with your score, similar to what you've noticed in K1 Logistics. We've gone ahead and taken note of this thread and will continue investigating any underlying issues that may be occurring. For any updates that may come from this report, we recommend viewing our Patch Notes as they become available, posted on the [url=https://www.bungie.net/7/en/News]News page[/url].