When you are reading a post in your timeline, there are various items of information, and ways to interact directly.
Click on the area 6 to open the post and see replies and other interaction. If you click a hashtag or a web link, you will open those rather than reply. Click on a blank area, or a simple word to see the replies.
Much like searching limitations on the Fediverse, showing replies has similar constraints. Your server is only showing replies that is has seen from other users it is aware of. You may not be seeing the entire story.
If you wish to see the complete posting history, scroll to the top of the post you have opened and click on “View on remote server”. This opens a new browser window and takes you to the user's server, which has a record of all interactions for the post.
Come back to your own server to reply.
The numbers being shown for Reply, Like, and Boost counts are only based on copies of this post that your own server is aware of elsewhere on the fediverse.
To see an accurate count, click the post as described above in 'Reading Replies', then click on “View on remote server” at the top.