You're seeing log/*/*/*.log because Splunk interprets the wildcard "greedily", i.e. it will match as much as possible.
There is no way that I know of to make the wildcards non-greedy, but there are workarounds that you can use. One is to specify explicitly that you want sources that match /logs/*/*.log but not /logs/*/*/*.log :
source="/logs/*/*.log" AND NOT source="/logs/*/*/*.log"
Or you could use regex to filter results, like below.
source="/logs/*/*.log" | regex source="/logs/[^/]+/[^.]+\.log"
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