This is expected IMAP/Gmail behavior rather than a Mailspring-specific issue. When someone replies to a thread, Gmail’s threading groups that reply with the original sent message — so the thread appears in both Inbox (because of the reply) and Sent Mail (because the original is there). Most email clients, including Thunderbird, show the same behavior. The reply itself should still appear in your Inbox; the thread just shows up in Sent because it contains your original message. There isn’t a way to suppress this without server-side filtering.
I’d be happy if it would appear in both inbox and sent folder however replys only appear in the sent folder in both Mailspring and Thunderbird. I haven’t noticed it this in Mailspring however in Thunderbird for a brief moment the incoming email will be in the inbox then it disappears and is in the sent folder.