How did my deleted iCloud photos end up in the new Photos app?
Note that iCloud.com/#photos is not the same thing as My Photo Stream, and photos that were only in My Photo Stream will not appear in iCloud.com/#photos. (Unless you turn on iCloud Photo Library and sync a Mac Photos library that contains the photos downloaded from My Photo Stream, which would then be uploaded to iCloud Photo Library.) So even though the photos were still in My Photo Stream, it would be expected that they would not appear on iCloud.com.

Deleting from My Photo Stream was, at least for a while, pretty buggy. And, at least when the feature was first made available (remember deleting was not available when My Photo Stream itself launched), "deleting" photos from it meant they were only erased from the device you were using at that moment and not actually removed from the stream.

Also note the following from Apple:


  After you delete a photo [from My Photo Stream], you might still see it on your iOS devices if it's more than 30 days old and you have fewer than 1000 photos in My Photo Stream.