Hello Anna,
This does in fact sound wrong. Whats important when you create your own process, is to ensure that you have entered all the data correctly. Especially make sure that all units and suppliers correspond to the article, and that the reference output corresponds to the output from the article.
If you are certain of this, then there are some further steps you can take.
1) Investigate the contribution tree from both processes, and evaluate directly if some of the processes should be more/less impactful.
2) Consult other analyses made, and see if their hotspot analyses match yours
3) Read the documentation for the processes you'd expect to be most impactful. Are they missing some steps? Do you need to add elementary flows manually?
I hope this helps, good luck in your search.