Mysqlでデータを外挿して配列に入れるにはどうすればよいですか？

これは括弧がない可能性があります。betweenをラップしてください 括弧による条件

$query = "SELECT * 
FROM earthquakes 
WHERE (milliseconds BETWEEN `$ieri` AND `$oggi`)
    AND (magnitude BETWEEN `$magn_min` AND `$magn_max`)
    AND (ipocentro BETWEEN `$ipo_min` AND `$ipo_max`)
OFFSET $offset LIMIT 400";

$n_quakes = "SELECT COUNT(*)
FROM earthquakes
WHERE (milliseconds BETWEEN `$ieri` AND `$oggi`)
   AND (magnitude BETWEEN `$magn`_min AND `$magn_max`)
   AND (ipocentro BETWEEN `$ipo_min` AND `$ipo_max`)
   AND (latitude BETWEEN `$lat_inf` AND `$lat_sup`)
   AND (longitude BETWEEN `$lng_sin` AND `$lng_des`)";