My organic group content node has this pathauto alias pattern:
[node:og-group-ref:1]/[node:og-group-ref:0]/[node:title]

When the node is saved the first time the alias is generated but misses [node:og-group-ref:1] part nonetheless the group audience field (og reference field) is saved with both group audience gids.
When editing the node a second time, and saving the node. The path auto alias displays as intended.

How can I update the node alias without manually resaving the node? Probably the node group audience field values are not all passed when the tokens get replaced when path auto alias is generated. And saving the second time the node the values are all available.