Hello @tferg155 ,

you have confugured Switch1 in the following manner:

spanning-tree mst configuration
name INE
revision 6767
instance 1 vlan 10, 20
instance 2 vlan 30, 40
instance 3 vlan 50, 60
!
>> spanning-tree mst 1-3 priority 24576

This means that this switch is root bridge for all MST instances 1 to 3 and as a result of this:

on Switch 2 you have:

Port Vlans in spanning tree forwarding state and not pruned
Po3 none

Po2 1,10,20,30,40,50,60

Each MST instance takes the same decision because the root bridge is the same for all of them.

There is nothing wrong in this. Each port-channel is seen as a single logical link by STP  ( any type inlcuding MST)

To be noted we don't know who is the root bridge of instance 0 the  IST instance but at the moment all your VLANs in use are associated to MST instances 1 to 3.

About your questions:

>> -and can the link aggregation cause a problem with mstp even if its well configured ?

No the two protocols work in combination with STP that sees each bundle as a logical link and sends its BPDU out a single member link , PAGP manages each single link by sending and receiving its own L2 PDUs.

to be noted nowdays LACP is to be preferred over PAGP,

.

>> do i need to open int vlan 10-60 with ip addresses on all the switch or just the core switch like im doing now is enough since the switch 2 and 3 are forwarding to the core 

Doing it on two switches of 3 ,  and using FHRP protocols like HSRP in each VLAN would provide default gateway redundancy to end users ( the HSRP VIP is different from SVI IP addresses but it is in the same IP subnet)

For a real world network would be a true benefit in lab it can be a chance to use HSRP or VRRP or GLBP.

Edit:

check who is the root bridge for instance 0, because all MST instances are actulally packed within a single BPDU with sections for each MST instance and the BPDU is asociated to instance 0 and all other MST instances.

show spanning-tree instance 0 detail

or

show spanning-tree mst instance 0 detail

Hope to help

Giuseppe