I use the image field with media module file selector. The inline entity form only saves the first image when cardinality is bigger than one.
I don't use Media, but would accept any patches that would fix this.
it seems the issue is caused by cleanupFieldFormState().
i'm not sure it should take place every time a IEF is submitted.
i also don't know if this could affects other fields and/or widgets, a more generic issue.
here is patch that calls the clean up only for Add IEFs, but i don't think this is the solution for this issue.
This fixed a similar issue for me where I had multiple *link* fields and only the first one was being saved / shown after editing.
I'm experiencing this issue with 7.x-1.3 as part of the latest Drupal Commerce Kickstart release (7.x-2.9). I first noticed the problem when I tried to edit several products in a single product display at the same time. I also noticed the problem occurred when editing the same product twice (edit product display, bring up IEF for a product, save IEF, re-open IEF for same product). In both situations, all fields with more than one value lost every value but the first.
Marked #2119253: ief referenced entity with a multi-value field is getting broken somewhere. as duplicate, looks related at least.
Unfortunately, vasike's patch is just a workaround.
Closing as a duplicate of #1846114: cleanupFieldFormState causes multivalue field rows to disappear since it has more complete instructions for reproducing, a better description of the current bug, and a better current patch.
Rolling my own patch ASAP.
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