To temporaly "solve" this issue, I've enabled LLDP on all switches.
But, this issue accours with other netboxes that doesn't have lldp protocol (like printers and some wireless devices). I've found on navtopology's debug log these errors that maybe point us to a solution:
DEBUG:nav.topology.vlan:could not find reverse edge for (<Netbox: y.x.250.134>, <Netbox: y.x.204.217>, <Interface: 5:18 at y.x.250.134>)
DEBUG:nav.topology.vlan:could not find reverse edge for (<Netbox: y.x.250.244>, <Netbox: y.x.162.81>, <Interface: Te1/14 at y.x.250.244>)
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What meaning these messages?