Online boarding passes for Star Alliance connecting flights

Probably everything is fine. You can try to check in on AC's website, there are cases where the checkin for each flight has to be done with the operating carrier. (I'm not sure if this works with Lufthansa's Amadeus code -- I believe AC has their own codes -- but you should be able to either find this in the booking confirmation or on checkmytrip.com. [EDIT: Since you checked in on AC for the outgoing flight, this would be the same code.]) It might be that this is only possible XX hours prior to the departure of the AC fight.

Another option is that AC wants to do some document check before handing you your boarding pass. In either case, I wouldn't be too concerned (as long as you have all required documents/eTA/...)

Given the flight time from India to Germany, this is probably a timing issue: the check in is not open for the AC flight at the time when you check in the LH flight.

I can guarantee that LH supports (some) interline check in with AC: I connected to AC in FRA from a European LH flight last month and had no problem with LH checking me in the AC flight and producing (electronic) boarding passes for all my flights, including AC flights. Of course the LH check in was much closer to the time of departure of my later connecting AC flight.

I’ve had some issues when the connecting flight is on another day as the departing flight (overnight stay on a single reservation), although travelling to Europe and connecting on the next day after the overnight flight has never been an issue.

There are some inconsistencies with the Air Canada checkin system. Just last year I booked via Air Canada a trip of 21 flights, made of 9 non-stop and 6 pairs of connecting flights, so this happened sometimes that I could not check in through those that were connecting flights but everything was OK.

First, as you did try the AC site. When you booked through them, that is the site that is most likely to work. Be careful though because they sometimes give you more than one Reference Number (for my 21 flight trip, I had 3), so you have to use the right one at the right time. All numbers were listed on the booking confirmation.

Checkin opens about 23 hours ahead of a flight. When you have a very long flight followed by another, it is possible the next one is still more than 23 hours away, so checkin will not be available. When you have a short and a long then, you may be able to check in one way but not the other because of this.

Sometimes they just can't do it. Although this did not apply to Lufthansa on any on my segments, one AC followed by 2 GOL domestic connections forced me to check in manually at the counter in Brazil.

You mention seat selection which was even spottier throughout my itinerary. I found that doing the selection via TAP Portugal was more success than others, even for non TAP flights (at least for those corresponding the the right reference number). Also they do let you select seats that got ignored by the next airline which happened when I connected from TAP to Thai Airways. This is compounded if you have airline status as some non-AC flight could see my level - and provide the privileges that come with it - but some did not.