"too short" means that the best alignments STAR found were too short to pass the filters.
This is controlled by --outFilterScoreMinOverLread --outFilterMatchNminOverLread which by default are set to 0.66. which means that ~2/3 of the total read length (sum of mates) should be mapped.
You can try to reduce these parameters to see how many more reads will be mapped.
One of the possibilities that you have short inserts, but it looks like you have trimmed the reads before mapping?
Also, you can try to map the reads 1 and 2 separately, to see if one of the reads is of poorer quality.