Hi @Leonie,
The difference is due to a bug in the bonding algorithm for molecules (which has been fixed but not deployed to the website yet).
Note that the atomic positions are correct and the same between both. The xyz file does not contain information on which atoms are bonded to which other atoms, so we have to work that out. There are many algorithms in pymatgen which try to answer the question of if two atoms are bonded. Unfortunately, the ones for molecules had a bug where atom labels were permuted leading to the wacky bonds shown. As mentioned, this has been fixed in pymatgen, and will be fixed on the next update to the website too.
Best,
Matt