Limitations: Though HDFS provide many features there are some areas where it doesn’t work well.

Low latency data access: Applications that require low-latency access to data i.e in the range of milliseconds will not work well with HDFS, because HDFS is designed keeping in mind that we need high-throughput of data even at the cost of latency.
Small file problem: Having lots of small files will result in lots of seeks and lots of movement from one datanode to another datanode to retrieve each small file, this whole process is a very inefficient data access pattern.