Duplicate data in MOR table Hudi

We see duplicate data in our hudi dataset

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**Describe the problem you faced**

A clear and concise description of the problem.

We run spark streaming application where we read kinesis stream process the data and stores in Hudi.
We started seeing duplicates in our hudi dataset
Below are our Hudi configs

DataSourceWriteOptions.TABLE_TYPE.key() -> DataSourceWriteOptions.MOR_TABLE_TYPE_OPT_VAL,
DataSourceWriteOptions.RECORDKEY_FIELD.key() -> "guid",
DataSourceWriteOptions.PARTITIONPATH_FIELD.key() -> "collectionName",
DataSourceWriteOptions.PRECOMBINE_FIELD.key() -> "operationTime",
HoodieCompactionConfig.INLINE_COMPACT_TRIGGER_STRATEGY.key() -> CompactionTriggerStrategy.TIME_ELAPSED.name,
HoodieCompactionConfig.INLINE_COMPACT_TIME_DELTA_SECONDS.key() -> String.valueOf(60 * 60),
HoodieCompactionConfig.CLEANER_POLICY.key() -> HoodieCleaningPolicy.KEEP_LATEST_COMMITS.name(),
HoodieCompactionConfig.CLEANER_COMMITS_RETAINED.key() -> "624",
HoodieCompactionConfig.MIN_COMMITS_TO_KEEP.key() -> "625",
HoodieCompactionConfig.MAX_COMMITS_TO_KEEP.key() -> "648",
HoodieCompactionConfig.ASYNC_CLEAN.key() -> "false",
HoodieCompactionConfig.INLINE_COMPACT.key() -> "true",
HoodieMetricsConfig.TURN_METRICS_ON.key() -> "true",
HoodieMetricsConfig.METRICS_REPORTER_TYPE_VALUE.key() -> MetricsReporterType.DATADOG.name(),
HoodieMetricsDatadogConfig.API_SITE_VALUE.key() -> "US",
HoodieMetricsDatadogConfig.METRIC_PREFIX_VALUE.key() -> "tacticalnovusingest.hudi",
HoodieMetadataConfig.ENABLE.key() -> "false",
HoodieWriteConfig.ROLLBACK_USING_MARKERS_ENABLE.key() -> "false",

We only use upsert in our code , we never use insert

dataframe.write.format("org.apache.hudi")
.option("hoodie.insert.shuffle.parallelism", hudiParallelism)
.option("hoodie.upsert.shuffle.parallelism", hudiParallelism)
.option(HoodieWriteConfig.TABLE_NAME, hudiTableName)
.option(DataSourceWriteOptions.OPERATION_OPT_KEY, DataSourceWriteOptions.UPSERT_OPERATION_OPT_VAL)
.option(HoodieMetricsDatadogConfig.METRIC_TAG_VALUES.key(), s"env:$environment")
.options(hudiOptions).mode(SaveMode.Append)
.save(s3Location)

Please help us on this.
Below are two situation where we see duplicates.
1. duplicates with same hudi commit time
2. duplicates with different commit time.

I have attached the json files for reference
We tried to delete duplicate data using hudi commit seq num and our primary key, it is deleting both keys
Duplicate with hudi DELETE
dataframe.write.format("org.apache.hudi")
.option("hoodie.insert.shuffle.parallelism", hudiParallelism)
.option("hoodie.upsert.shuffle.parallelism", hudiParallelism)
.option(DataSourceWriteOptions.OPERATION_OPT_KEY, DataSourceWriteOptions.DELETE_OPERATION_OPT_VAL)

We tried to deduplicate with the hudi cli command,

repair deduplicate --duplicatedPartitionPath s3://**/ --repairedOutputPath s3://**/ --sparkMemory 2G --sparkMaster yarn

We are getting java.io.FileNotFoundException:
Please help

**Expected behavior**

A clear and concise description of what you expected to happen.

**Environment Description**

* Hudi version : 0.11.1

* Spark version : 3.2

* Hive version :NA

* Hadoop version : NA

* Storage (HDFS/S3/GCS..) :S3

* Running on Docker? (yes/no) :no

Start with the Hudi 0.11.1 MOR-table configuration and Spark 3.2 write options shown in the issue, then investigate the two duplicate scenarios and the CLI `repair deduplicate` FileNotFoundException. Reproduce against the stated S3 environment if possible; done should include a confirmed cause, corrected behavior, and verification that deduplication no longer removes both records.

Written by the indexing model from the issue text.