There's really nothing you need to change. Many words in English have multiple meanings, and native speakers become quite used to figuring out from context which is intended:
I missed the bus
means you didn't get on it. The past tense establishes this is an action that has already happened, and by default, the listener will interpret this as "I failed to catch the bus".
English speakers use the present tense to describe regular or repeated action. Something like
I often miss the bus (because my alarm is broken)
would not be ambiguous, especially with "often", as that establishes the frequency of the action. A native speaker will know this means you regularly fail to catch the bus.
However if you say something like:
I miss the (old) bus
any native should know you intend the other meaning, "I have fond memories of the (old) bus". In this context, there is no adverb to establish frequency, plus the use of "old" establishes you are talking about something you remember.
Naturally this is not foolproof. For example:
I missed my friend.
Does this mean you failed to meet up with your friend, or that you used to have fond memories of your friend? We don't know without context:
I missed my friend so much (I got her a job in our home town so she would move back.)
The "so much" is enough to establish we're talking about nostalgia or longing to see someone.
I just missed my friend (at the train station -- she left right before I arrived.)
The "just" is enough to establish a the time frame, and indicate that you failed to meet up with your friend.