Perhaps you can elaborate a bit on what you mean by unexpected output? If the files are of the same type and have the same schema stacking them should not be problematic.
If it is then you would want to use a code recipe to read each one and add them to a dataset.
Here is an example this would give you more flexibility to process exclude lines etc from each file using pandas. If you are using a local filesystem managed folder, if you are using a remote folder( e.g S3) you will need to use get_download_stream(). Instead.
from dataiku import pandasutils as pdu
import pandas as pd
# Get DSS client
client = dataiku.api_client()
# Get managed folder
project = client.get_project(dataiku.default_project_key())
managed_folder = dataiku.Folder("27jITy2p")
# Get path to managed folder on disk
path = managed_folder.get_path()
l = [pd.read_csv(filename) for filename in glob.glob(path+ "/*.csv")]
df = pd.concat(l, axis=0)
#Write recipe outputs
merged_orders = dataiku.Dataset("merged_orders")