This KB explains a behavior observed on QFX5120-48Y where changing a configuration causes link flaps on interfaces that are unrelated to that configuration. Specifically, this issue occurs when the speed auto setting is explicitly configured.

On QFX5120-48Y using SFP+-10G-SR, for example, when VLAN10 is removed from ae24, a different physical interface flaps. This issue occurs consistently. Below are the logs captured during the event:

labroot@Switch# show | compare rollback 1
[edit interfaces ae24 unit 0 family ethernet-switching vlan]
-       members [ VLAN2500-2599 VLAN2600-2699 ];
+       members [ VLAN2500-2599 VLAN2600-2699 VLAN10 ];

labroot@Switch# commit

Oct 24 06:22:08  Switch kernel: lag_bundlestate_ifd_change: bundle ae0: bundle IFD minimum bandwidth or minimum links not met, Bandwidth (Current : Required) 0 : 1 Number of links (Current : Required) 0 : 1
Oct 24 06:22:08  Switch kernel: lag_bundlestate_ifd_change: bundle ae100: bundle IFD minimum bandwidth or minimum links not met, Bandwidth (Current : Required) 0 : 1 Number of links (Current : Required) 0 : 1
Oct 24 06:22:08  Switch kernel: lag_bundlestate_ifd_change: bundle ae104: bundle IFD minimum bandwidth or minimum links not met, Bandwidth (Current : Required) 0 : 1 Number of links (Current : Required) 0 : 1
Oct 24 06:22:08  Switch kernel: lag_bundlestate_ifd_change: bundle ae4: bundle IFD minimum bandwidth or minimum links not met, Bandwidth (Current : Required) 0 : 1 Number of links (Current : Required) 0 : 1
Oct 24 06:22:08  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 523, ifAdminStatus down(2), ifOperStatus down(2), ifName ae0.0
Oct 24 06:22:08  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 539, ifAdminStatus up(1), ifOperStatus down(2), ifName ae0
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 542, ifAdminStatus down(2), ifOperStatus down(2), ifName ae100.0
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 541, ifAdminStatus up(1), ifOperStatus down(2), ifName ae100
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 554, ifAdminStatus down(2), ifOperStatus down(2), ifName ae104.0
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 553, ifAdminStatus up(1), ifOperStatus down(2), ifName ae104
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 581, ifAdminStatus down(2), ifOperStatus down(2), ifName ae4.0
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 580, ifAdminStatus up(1), ifOperStatus down(2), ifName ae4
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 520, ifAdminStatus down(2), ifOperStatus down(2), ifName xe-0/0/0.0
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 598, ifAdminStatus down(2), ifOperStatus down(2), ifName xe-0/0/0.32767
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 599, ifAdminStatus down(2), ifOperStatus down(2), ifName xe-0/0/4.0
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 600, ifAdminStatus down(2), ifOperStatus down(2), ifName xe-0/0/4.32767
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 589, ifAdminStatus down(2), ifOperStatus down(2), ifName xe-1/0/0.0
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 590, ifAdminStatus down(2), ifOperStatus down(2), ifName xe-1/0/0.32767
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 591, ifAdminStatus down(2), ifOperStatus down(2), ifName xe-1/0/4.0
Oct 24 06:22:09  Switch mib2d[21138]: SNMP_TRAP_LINK_DOWN: ifIndex 592, ifAdminStatus down(2), ifOperStatus down(2), ifName xe-1/0/4.32767
Oct 24 06:22:12  Switch mib2d[21138]: SNMP_TRAP_LINK_UP: ifIndex 539, ifAdminStatus up(1), ifOperStatus up(1), ifName ae0
Oct 24 06:22:12  Switch mib2d[21138]: SNMP_TRAP_LINK_UP: ifIndex 580, ifAdminStatus up(1), ifOperStatus up(1), ifName ae4
Oct 24 06:22:12  Switch mib2d[21138]: SNMP_TRAP_LINK_UP: ifIndex 541, ifAdminStatus up(1), ifOperStatus up(1), ifName ae100
Oct 24 06:22:12  Switch mib2d[21138]: SNMP_TRAP_LINK_UP: ifIndex 553, ifAdminStatus up(1), ifOperStatus up(1), ifName ae104

This issue occurs when the 'speed auto' setting is explicitly configured on the interfaces.

set interfaces xe-0/0/X speed auto

On the QFX5120-48Y with SFP+-10G-SR, this configuration is not required, and explicitly setting may lead to unexpected behavior like this.
Therefore, removing this option from the configuration resolved the issue.
For details on auto-negotiation support, please refer to the following document:

https://www.juniper.net/documentation/us/en/software/junos/cli-reference/topics/ref/statement/speed-edit-interfaces-ethernet.html#id-speed-ethernet__d888174e333