Hi.
You need to define the number of aggregated Ethernet interfaces to be created on the Juniper switch as well (not sure if you have it done):
user@EX2200# set chassis aggregated-devices ethernet device-count 1
user@EX2200# commit
Setting the number to 1 allows to create interface ae0.
The documentation for LAG link on EX series:
https://www.juniper.net/documentation/en_US/junos/topics/task/configuration/link-aggregation-cli.html
The cabling and speed/duplex can be other culprits. Your post indicates the both links were up as "standalone" links. This should exclude cabling issues. The vlan 3 does exist in VLAN DB of both switches as well.
I would try to troubleshooting steps in following order:
1) define count of aggregated links on EX2200 (see above) and commit
2) manually define the speed on EX2200 LAG interface (ae0) and Cisco C3550 Po1 to 100Mb/s
user@EX2200# set interfaces ae0 aggregated-ether-options link-speed 100m
user@EX2200# commit
user@C3550(config)# interface Port-channel1 user@C3550(config-if)# speed 100
This can however introduces issues (Cisco C3550 doesn't support MDIX, auto-negotiation might be required).
Hope this helps a bit.
Regards
Luděk