In my case, I had multiple extension targets and multiple metafields defined in the toml file. I reviewed new guidance at https://shopify.dev/docs/apps/app-extensions/configuration .
What fixed the problem for my app was modification to the toml file to:
a) use [[extensions.targeting.metafields]] instead of [[extensions.metafields]] and
b) place each metafield block under the associated target block.
Example:
[[extensions.targeting]]
module = “./src/Checkout1.jsx”
target = “purchase.checkout.shipping-option-list.render-before”
[[extensions.targeting.metafields]]
key = “key1”
namespace = “custom”
[[extensions.targeting]]
module = “./src/Checkout2.jsx”
target = “purchase.checkout.shipping-option-list.render-after”
[[extensions.targeting.metafields]]
key = “key2”
namespace = “custom”