I have my local comic shop save back a few comics for me each month because I travel for my job and can't make it there frequently. Also, they give me a decent discount on the one's I have held. I show up on Wednesday and they are sold out of CAP #25 so, I don't get my issue. This has happened a few times. The last time it happened I told the owner "If nothing else, make sure I get my Cap comic". What the shop does is set out new comics for the general public and whatever comics don't sell that day go into the saved bin. There's been a few times where they were sold out of the comic I had saved but they held back comics for me that I could care less about. I'm a nice guy; if it looked interesting enough I would go ahead and buy it. I had a subscription for years. But, I like going to this shop now and again so, I thought I might as well give him more business. Is this common practice? The owner's a nice guy but it seems disrespectful to me.
I'm in a similar position to you. My comic shop is an hour's drive away, and sometimes it's two or three months before I can get there to pick up my subscription issues from the pull list. Now as part of the subscription arrangement, I had to put a desposit of $20 to the store, which they keep until the day I cancel my subscription issues. So that obliges them to hold my issues. After seeing Cap 25 sell for stupidly high prices, I called my store to see what they had in my sub box, and if they had 'misplaced' my Cap 25. They still had it. Good for them. Your store owner owes you an apology. I wonder if they were selling them on ebay.