One or More Analysis Steps Not Performed via API `load()`: Data References Missing

[utkonos]

Version and Platform (required):

• Binary Ninja Version: 5.3.8837-dev Ultimate, d2d9934a
• OS: macos
• OS Version: 26.2.0
• CPU Architecture: arm64

Bug Description:
The analysis results are different if you open a file in GUI vs loading the exact same file using the API. Specifically, data references are missing.

Steps To Reproduce:

1. Open file in GUI: geometric badge clones simply
2. Save database.
3. Open file using API load() via code below.
4. Compare to exactly same code, but open the GUI created database.

import pathlib
import sys
sys.path.append('/Applications/Binary Ninja.app/Contents/Resources/python')
import binaryninja
bv = binaryninja.load('0ba5fb69df06f6e84191861f8e7988c97c637f7c1c4220016e337418916557bb')
bv.update_analysis_and_wait()
f = bv.get_function_at(0x7ff6c4a472a0)
print(f.name)
refs = bv.get_data_refs(f.start)
print(list(refs))

VS

import pathlib
import sys
sys.path.append('/Applications/Binary Ninja.app/Contents/Resources/python')
import binaryninja
bv = binaryninja.load('foo.bndb')
bv.update_analysis_and_wait()
f = bv.get_function_at(0x7ff6c4a472a0)
print(f.name)
refs = bv.get_data_refs(f.start)
print(list(refs))

Expected Behavior:
Same analysis in equivalent BNDBs.

Screenshots:
GUI:

API:

Binary:
geometric badge clones simply