You need to consider the minimum change times.
For example, at Nässjö Centralstation, the indicated minimum change time is generally 10 minutes. If you have a through ticket with a change at Nässjö C, you will be given a connection with at least 10 minutes to change. For other connections, the recommended time is even longer, such as 30 minutes from Snälltåget to SJ or 60 minutes if the SJ train is snabbtåg. If you try your own connection with only 3 minutes, the risk is on you and there is no warranty if you miss your connection. However, if the train you are connection to is a regional train, your ticket may be valid for the next train on the same line; check your ticket conditions for details.
In Vaggeryd the minimum connection time is 5 minutes, so a 3-minute connection is still not valid. It would be valid at Vaggaryd Torsbo, but that is a bus stop.
Most traffic search engines respect minimum change times. However, in the past I have seen Google Transit (Google Maps) suggest "unsupported" changes. I don't know if Google still has this bug.
(IMHO, requiring 30, 60, or even 120 minutes at Nässjö is rather crazy, but this is what it says in the database for certain connections.)