@Šimon Říha Thank you for reaching out to us. As I understand you are trying to get the complete list of TI indicators using MS Security Graph API.
Would request you to try to add ConsistencyLevel: eventual in the request headers section and verify the output if it helps or not.
Reference: https://learn.microsoft.com/en-us/graph/aad-advanced-queries?tabs=http
Let me know if you have any further questions, if required we can connect offline and troubleshoot further.
Please remember to "Accept Answer" if answer helped, so that others in the community facing similar issues can easily find the solution.