I am at my wits end trying to figure out what is going wrong - I saved roughly 35 waypoints using my garmin instinct a few days ago, and only one of the waypoints will export to a KML or show up in the garmin explore web app. All 35 waypoints are visible on the sidebar and can be selected, and I can change the display icon for the invisible waypoints. All of the waypoints show up correctly in the Garmin Explore iOS app. Somehow, changing the icon for an invisible waypoint in the web app does change the icon in the explore iOS app (after a sync). But still nothing visible in the web app. Selecting all waypoints and attempting to export to a KML file results in only the visible point being exported.
If I recall correctly, the point that does display correctly was saved through the Garmin Explore iOS app directly, while the remaining waypoints were all saved using the Instinct watch directly (holding down the GPS button, then saving as a waypoint after the coordinate drift settled down). The correctly-displaying waypoint has an auto-label formated "May 20, 2022, 6:01 PM" while the subsequent waypoints are auto-labeled in a different format: "20 MAY 6:04p" and so on.
I suspect there's some incompatibility between the formatting of these instinct-written waypoints and the explore.garmin.com/map page itself, since they only seem to behave strangely on that page.
In case anybody else has this problem and needs to export their waypoints for use in a different mobile app (or for GIS applications) - I was able to identify a viable (if tedious) workaround. This workaround involves use of the Gaia GPS iOS app (I use the free version, not a subscription). In the Garmin Explore iOS app (or the web map), select all of the non-displaying waypoints and add them to a group. From the iOS app, open the Library tab and navigate down to this group (should be in "Collections" at the bottom of the page). Select the group and confirm that the waypoints are displayed on the mini-map and listed below the mini-map. Hit the ". . ." button at the top-right of the page, then select "Share." Choose "Gaia GPS" from the available apps in the share menu, or go over to "More" and find it in the longer app list. Open Gaia GPS, and after a few moments you should see a folder with the same name as the folder you shared from the Garmin app. Select this folder in Gaia GPS, confirm that the waypoints are in the list, then select "Share" from the top of the folder view. The bottom option on the "Share Folder" menu in Gaia GPS should be "Export File" - you can save out a GPX, KML, or GeoJSON from here. I exported a KML to my iPhone's files, then copied it from there to iCloud Drive, and downloaded it to my PC. This KML imported correctly into ArcGIS and all waypoints were visible.
I hope this is just a bug that can be identified and corrected based on my description; if not, I at least hope anyone else experiencing this issue is able to work around it using Gaia GPS (or another iOS app) so that their collected waypoints aren't rendered useless.\
Cheers!