It is extremely difficult to say anything sensible about this question, without actually having the full traceroutes and the real IP addresses. Please don't obscure data like this - IP addresses are not secrets.
Having said that, the only case where I can see this happening is when the destination IP addresses are simply not the same. Per-packet load balancing is sometimes done on (parts of) links, which can cause partial failures. However, then both traceroutes should show failures - not consistently just one of them.
So, given that the destination IP addresses are different, my best guess is that one of the destination IP addresses is simply not configured, or uses a stricter firewall. Traceroute will keep trying to look further until it receives a reply from the target host. If the target host does not exist or refuses to reply, traceroute will go on until it reaches it's limit, for which 30 hops is a common setting.