Yes, I reckon that is the problem. At first glance, your description looks very spammy. At least to me, who has spent a lot of time in SEO efforts. I can imagine a reviewer at Google taking one look and saying "that's spam".
Maybe changing it to a list format might work better? Like this:
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Stop Alarm works with all public transportation systems here in the United States, it’s great for daily commuters on all of the following networks:
- MBTA
- Muni Metro
- Metro, MetroRail
- Max light Rail
- SEPTA, DART & Denver RTD
- UTA TRAX
- Metrolink, Central Link & VTA Light Rail
- The T
- RTA Streetcars
- Newark Light Rail
- LYNX
- Portland Streetcar, River Line & Sprinter
- Tide Light Rail
- Memphis RTA Trolley
- Tacoma Link, TECO Line Streetcars
- Kenosha Transit, PATCO
and almost every other rail, bus, or trolley system in the country.
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That looks a little less spammy to me, even though it's the same content. Ultimately though Google seems to take a pretty hard stance on "keyword stuffing" as they call it. You might just have to reduce the number of keywords you use - as much as it will hurt your rankings!